Detection of T Cell Exhaustion or Lack of T Cell Costimulation and Uses Thereof

Abstract

The application relates to methods of assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, and the use of such methods in determining an individual's risk of autoimmune disease progression, progression of a chronic infection, not responding to a treatment for a chronic infection, not mounting an effective immune response to vaccination, infection-associated immunopathology, transplant rejection, or cancer progression. The application also relates to in vitro methods for assessing whether CD8.sup.+ and CD4.sup.+ T cells in a sample have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, and for identifying a substance capable of inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in an individual, as well as a kit for assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype or whether an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is present in a sample of CD8.sup.+ and CD4.sup.+ T cells.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application is a continuation-in-part of International Patent Application No. PCT/GB2016/051385, filed on May 13, 2016, designating the United States of America, which derives priority from GB 1508419.7, filed on May 15, 2015. Each of the above-referenced applications is incorporated by reference herein in its entirety.

FIELD OF THE INVENTION

[0002] The present invention relates to methods of assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, and the use of such methods in determining an individual's risk of autoimmune disease progression, progression of a chronic infection, not responding to a treatment for a chronic infection, not mounting an effective immune response to vaccination, infection-associated immunopathology, transplant rejection, or cancer progression. Such methods may also be used to guide treatment of autoimmune diseases, chronic infections, infection-associated immunopathology, transplant patients, and cancer. The present invention also relates to in vitro methods for assessing whether CD8.sup.+ and CD4.sup.+ T cells in a sample have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, and for identifying a substance capable of inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in an individual, as well as a kit for assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype or whether an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is present in a sample of CD8.sup.+ and CD4.sup.+ T cells.

BACKGROUND TO THE INVENTION

[0003] Following transient exposure to antigen, such as during acute viral infection, antigen-specific T cells undergo rapid proliferation followed by a more prolonged contraction. Following this, the persistent population of memory cells that remain confer protective immunity, characterised by higher proliferative potential and a reduced activation threshold (E. J. Wherry, R. Ahmed, Journal of virology 78, 5535-5545, 2004). However, where antigen persists or accessory costimulatory signals are limiting, such as during chronic viral infection, CD8 T cells develop a hierarchical loss of function in a process termed "exhaustion" (A. J. Zajac et al., The Journal of experimental medicine 188, 2205-2213, 1998). In models of acute antigen exposure, the primary CD8 response is equivalent in the absence of accessory CD4 costimulation, although long-term memory responses rely upon it (D. J. Shedlock, H. Shen, Science 300, 337-339, 2003; J. C. Sun, M. J. Bevan, Science 300, 339-342, 2003). In chronic antigen exposure, CD8 responses--and memory responses in particular--are exquisitely dependent on the provision of CD4 help (E. E. West et al., Immunity 35, 285-298, 2011). Consequently, in both mice and in humans, the presence of CD4 help results in enhanced viral clearance and resolution of chronic infection while also promoting robust memory responses in acute infection (R. D. Aubert et al., J Exp Med 194, 1395-1406, 2001).

[0004] The dysfunctional state of exhaustion was originally identified in a chronic form of murine LCMV infection as cells showing reduced cytokine production (A. J. Zajac et al., The Journal of experimental medicine 188, 2205-2213, 1998) with hierarchical loss of IL2 production and cytolytic killing followed by loss of TNF production and, finally, deletion of antigen-specific cells (D. Moskophidis et al., Nature 362, 758-761, 1993). More recently it has been shown that this progressive dysfunction is accompanied by profound changes in gene expression, distinct from those seen in effector or anergic cells (E. J. Wherry et al., Immunity 27, 670-684, 2007; I. A. Parish et al., Blood 113, 4575-4585, 2009). This transcriptional `signature` of CD8 exhaustion is both characterised and driven by non-redundant patterns of inhibitory receptor coexpression (S. D. Blackburn et al., Nature immunology 10, 29-37, 2009) that can serve as both biomarkers of viral progression (C. L. Day et al., Nature 443, 350-354, 2006) and targets for therapy, helping to restore viral control (D. L. Barber et al., Nature 439, 682-687, 2006).

[0005] Exhausted T cell responses have likewise been implicated in loss of immunological control of cancers (H. W. Virgin et al., Cell 138, 30-50, 2009). A signature of CD8 T cell exhaustion has been described within the tumour microenvironment (Baitsch et al., JCI, 121(6):2350, 2011) and exhaustion-associated inhibitory receptor blockade (known as `checkpoint blockade`) has shown promise in clinical trials (Topalian et al., N Engl J Med 366, 2443-245; Pardoll, Nat Rev Cancer 12:252, 2012; Phan et al. PNAS100:8372-7, 2003).

[0006] It has also been speculated that a similar phenotype of exhaustion may be seen in the context of organ or tissue transplantation (Valujskikh A, Li X C., Curr Opin Organ Transplant. 2012, 17:15-19), due primarily to the known role of exhaustion-associated inhibitory receptors in the process of immunoregulation (Thorp et al. Curr Opin Org Transplant 2015, 20(1):37-42). While small, studies in murine transplant models have argued that T cell exhaustion may limit acute rejection (Steger et al., Transplantation. 2008, 85:1339-1347) or chronic rejection (Sarraj et al., Proc Natl Acad Sci USA. 2014; 111:12145-12150).

[0007] The process of T cell exhaustion has also been implicated in the success of vaccination strategies. The goal of vaccination is to produce long-lasting, antigen-specific immunity that will protect the subject from infection, to eradicate an existing infection or, in the case of cancer vaccines, to eradicate a tumour. During persistent infection, blockade of exhaustion-associated pathways allows an otherwise ineffective vaccine to successfully enhance viral clearance (Brooks et al. JEM 2008, 205(3):533-41).

[0008] In chronic viral infection higher levels of CD4 help are associated with diminished CD8 T cell exhaustion (Thimme et al., J Exp Med 194, 1395-1406, 2001; Aubert et al., Proc Natl Acad Sci USA 108, 21182-21187), while during vaccination, costimulation promoted by adjuvants, can encourage long-lasting immune responses (Reed et al., Nat Med 2013; 19: 1597-1608). The potential for adjuvants to encourage such a protective response has been known for almost a century (Glenny et al., J Pathol Bacteriol 1926; 29: 38-45). However, it remains unclear which adjuvants provide optimal protection (Reed et al., Nat Med 2013; 19: 1597-1608). Reversing exhaustion-associated inhibitory pathways through targeted costimulation or inhibitory receptor blockade has shown some promise in maintaining effective immune responses (Wang et al., Cell Mol Immunol 2014; Vezys et al., J Immunol 2011; 187: 1634-1642).

[0009] A role for individual exhaustion-associated inhibitory receptors in autoimmunity has also been demonstrated--both through GWAS association results (Gateva et al., Nat Genet 41, 1228-1233, 2009; Lee et al Lupus 18, 9-15, 2009; Prokunina et al., Nat Genet 32, 666-669, 2002) and functional studies in mice, showing an increasingly severe phenotype in their absence (Keir et al., Annu Rev Immunol 26, 677-704, 2008; Rangachari, et al., Bat3 promotes T cell responses and autoimmunity by repressing Tim-3-mediated cell death and exhaustion. Nat Med; Okazaki et al., PD-1 and LAG-3 inhibitory co-receptors act synergistically to prevent autoimmunity in mice. J Exp Med 208, 395-407).

[0010] The underlying process of T cell exhaustion has been implicated in each of the contexts outlined above. As a result there is substantial and increasing interest in either reversing (in cancer, chronic infection or vaccination), preventing (in vaccination) or promoting the process (in autoimmune and infection-associated immunopathology and transplantation) to improve clinical outcomes for patients. Although recent progress has been made in both chronic infection (Day et al. Nature 2006; 443:350) and cancer (Herbst et al. Nature 2014; 515:563), there currently exists no method of measuring T cell exhaustion that is sufficiently robust or validated to allow prediction of outcome, response to therapy or to allow targeted therapy in patients with infection, cancer, autoinfection-associated immunopathology or who are receiving a vaccination or a transplant. K(lysine) acetyltransferase 2B (KAT2B), also known as P300/CBP-associated factor (PCAF), was originally identified as a histone acetyltransferase, which promotes cell-cycle arrest and counteracts the mitogenic influence of the adenoviral E1A oncoprotein (Yang, Xiang-Jiao et al. Nature 1996; 382:319-24). In addition, KAT2B has been shown to mediate an anti-apoptotic effect under conditions of metabolic stress (Xenaki, G. et al. Oncogene 2008; 27:5785-96), increasing cellular resistance to cytotoxic compounds when overexpressed (Hirano et al. Mol Cancer Research 2010; 8(6):864-72). KAT2B contains both bromodomain and histone acetyltransferase regions, which confer the capacity to both `read` and `write` epigenetic marks and act as a transcriptional co-activator. KAT2B has also been described as playing a role in hepatic gluconeogenesis, glucose metabolism and glucose homeostasis and has been proposed as target for diabetes treatment (Annicotte J.-S., 2014 Seminar Of The Lausanne Integrative Metabolism And Nutrition Alliance; Annicotte et al., 2013, Diabetes and Metabolism, 39(S1):Al2; Sun et al., 2014 Cell Rep. 24; 9(6):2250-62; Ravnskjaer et al. 2013 J Clin Invest. 123(10): 4318-4328; WO2014/037362; WO2013/148114). KAT2B has also been proposed as a marker of autoimmune disease progression (WO2010/084312) but has not been linked with an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype.

SUMMARY OF THE INVENTION

[0011] The present inventors have identified gene expression signatures that can be used to identify an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, or a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype. Identification of these phenotypes in individuals is expected to be useful in assessing an individual's risk of: autoimmune disease progression, progression of a chronic infection, not responding to a treatment for a chronic infection, not mounting an effective immune response to a vaccine, infection-associated immunopathology, transplant rejection, or cancer progression, as well as guiding therapy in autoimmune diseases, chronic infection, vaccination, infection-associated immunopathologies, transplantation, and cancer.

[0012] An aspect of the invention provides a method of assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype. The method comprises establishing, by determining the expression level of two more genes selected from the group consisting of:

[0013] K(lysine) acetyltransferase 2B gene (KAT2B);

[0014] calcium/calmodulin-dependent serine protein kinase 3 gene (CASK);

[0015] ATP-binding cassette sub-family D member 2 gene (ABCD2);

[0016] disks large homolog 1 gene (DLG1);

[0017] synovial sarcoma translocation, chromosome 18 gene (SS18);

[0018] Retinoblastoma-like protein 2 gene (RBL2);

[0019] RAS oncogene family-like 1 gene (RAB7L1);

[0020] methylenetetrahydrofolate dehydrogenase 1 gene (MTHFD1);

[0021] keratoca gene (KERA);

[0022] B cell-specific Moloney murine leukemia virus integration site 1 gene (BMI1);

[0023] conserved oligomeric Golgi complex subunit 5 gene (COG5);

[0024] cAMP-specific 3',5'-cyclic phosphodiesterase 4D gene (PDE4D); and

[0025] variable charge, Y-linked gene (VCY);

[0026] in a sample obtained from the individual, whether said subject has said phenotype,

[0027] wherein said phenotype is characterised by upregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and downregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype.

[0028] Other aspects of the invention provide methods of assessing whether an individual is at high risk or low risk of autoimmune disease progression, progression of a chronic infection, not responding to a treatment for a chronic infection, not mounting an effective immune response to vaccination, infection-associated immunopathology, transplant rejection, or cancer progression, as set out in the claims.

[0029] Yet other aspects of the invention provide methods of treating, or selecting for treatment, individuals who have been identified using a method of the invention as being at high risk or low risk of autoimmune disease progression, progression of a chronic infection, not responding to a treatment for a chronic infection, infection-associated immunopathology, cancer progression, not mounting an effective immune response to vaccination, or transplant rejection, employing a method as set out above, as set out in the claims. Treatment may comprise inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, or inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype, in the individual, as appropriate, to decrease the risk of autoimmune disease or cancer progression, progression of a chronic infection, not responding to a treatment for a chronic infection, infection-associated immunopathology, transplant rejection, or not mounting an effective immune response to vaccination.

[0030] An in vitro method for assessing whether CD8.sup.+ and CD4.sup.+ T cells in a sample have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, and an in vitro method for identifying a substance capable of inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in an individual, as set out in the claims, are similarly provided as aspects of the invention, as is a method of preparing CD8.sup.+ T cells with an exhausted or non-exhausted CD8.sup.+ T cell phenotype.

[0031] A kit for assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, or whether an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is present in a sample of CD8.sup.+ and CD4.sup.+ T cells forms a further aspect of the invention.

[0032] The following numbered paragraphs set out additional embodiments of the invention.

[0033] Paragraph 1. A method of assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising establishing, by determining the expression level of two more genes selected from the group consisting of:

[0034] K(lysine) acetyltransferase 2B gene (KAT2B);

[0035] calcium/calmodulin-dependent serine protein kinase 3 gene (CASK);

[0036] ATP-binding cassette sub-family D member 2 gene (ABCD2);

[0037] disks large homolog 1 gene (DLG1);

[0038] synovial sarcoma translocation, chromosome 18 gene (SS18);

[0039] Retinoblastoma-like protein 2 gene (RBL2);

[0040] RAS oncogene family-like 1 gene (RAB7L1);

[0041] methylenetetrahydrofolate dehydrogenase 1 gene (MTHFD1);

[0042] keratocan gene (KERA);

[0043] B cell-specific Moloney murine leukemia virus integration site 1 gene (BMI1);

[0044] conserved oligomeric Golgi complex subunit 5 gene (COG5);

[0045] cAMP-specific 3',5'-cyclic phosphodiesterase 4D gene (PDE4D); and

[0046] variable charge, Y-linked gene (VCY);

[0047] in a sample obtained from the individual, whether said subject has said phenotype,

[0048] wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype.

[0049] Paragraph 2. A method of assessing whether an individual is at high risk or low risk of autoimmune disease progression, the method comprising:

[0050] (i) determining whether the individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype using the method of paragraph 1,

[0051] wherein the presence of said phenotype indicates that the individual is at low risk of autoimmune disease progression, and

[0052] wherein the absence of said phenotype indicates that the individual is at high risk of autoimmune disease progression.

[0053] Paragraph 3. A method of assessing whether an individual is at low risk or high risk of autoimmune disease progression, by determining whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising:

[0054] (i) providing a PBMC sample obtained from the individual;

[0055] (ii) extracting mRNA from the PBMC sample;

[0056] (iii) performing reverse transcription quantitative PCR (RT-qPCR) to convert the mRNA into cDNA and determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0057] wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype, and

[0058] wherein the presence of said phenotype indicates that the individual is at low risk of autoimmune disease progression, and

[0059] wherein the absence of said phenotype indicates that the individual is at high risk of autoimmune disease progression.

[0060] Paragraph 4. The method according to any one of Paragraphs 2 to 3, wherein the autoimmune disease is not rheumatoid arthritis (RA) or inflammatory bowel disease (IBD).

[0061] Paragraph 5. The method according to Paragraph 4, wherein the autoimmune disease is selected from the group consisting of: ANCA-associated vasculitis (AAV), systemic lupus erythematosus (SLE), type 1 diabetes, and idiopathic pulmonary fibrosis (IPF).

[0062] Paragraph 6. The method according to any one of Paragraphs 2 to 5, wherein the autoimmune disease is AAV or SLE, and

[0063] wherein an individual who is at low risk of autoimmune disease progression is at low risk of relapses or flares of the disease, and

[0064] wherein an individual who is at high risk of autoimmune disease progression is at high risk of relapses or flares of the disease.

[0065] Paragraph 7. The method according to Paragraph 2 to 5, wherein the autoimmune disease is type 1 diabetes, and

[0066] wherein an individual who is at low risk of autoimmune disease progression is at low risk of progressing to type 1 diabetes, and

[0067] wherein an individual who is at high risk of autoimmune disease progression is at high risk of progressing to type 1 diabetes.

[0068] Paragraph 8. The method according to any one of Paragraphs 2-5, wherein the autoimmune disease is IPF, and

[0069] wherein an individual who is at low risk of autoimmune disease progression is at low risk of ongoing reduction of lung function, and

[0070] wherein an individual who is at high risk of autoimmune disease progression is at high risk of ongoing reduction of lung function.

[0071] Paragraph 9. An autoimmune disease progression risk assessment system for use in a method as defined in any one of Paragraphs 2 to 8, the system comprising a tool or tools for determining expression of two more genes selected from the group consisting of:

[0072] KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY;

[0073] and a computer programmed to compute an autoimmune disease progression risk score from the gene expression data of the subject.

[0074] Paragraph 10. The method according to any one of Paragraphs 2 to 8, further comprising:

[0075] (ii) selecting an individual identified as one who is at high risk or low risk of autoimmune disease progression in step (i) for treatment for the autoimmune disease.

[0076] Paragraph 11. The method according to any one of Paragraphs 2 to 8, further comprising:

[0077] (ii) subjecting an individual identified as one who is at high risk or low risk of autoimmune disease progression in step (i) to treatment for the autoimmune disease.

[0078] Paragraph 12. A method for treating an autoimmune disease in an individual, the method comprising:

[0079] (i) identifying the individual as one who is at high risk or low risk of autoimmune disease progression using a method according to any one of Paragraphs 2 to 8, and

[0080] (ii) subjecting the individual to treatment for the autoimmune disease.

[0081] Paragraph 13. A method for treating an autoimmune disease in an individual, the method comprising:

[0082] (i) requesting a test providing the results of an analysis to determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0083] in a sample obtained from the individual,

[0084] wherein downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual has said phenotype, and

[0085] wherein upregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and downregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual does not have said phenotype, and

[0086] wherein the presence of said phenotype indicates that the individual is at low risk of autoimmune disease progression, and

[0087] wherein the absence of said phenotype indicates that the individual is at high risk of autoimmune disease progression,

[0088] (ii) treating the individual for the autoimmune disease.

[0089] Paragraph 14. The method according to any one of Paragraphs 10 to 13, wherein the treatment comprises inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in the individual.

[0090] Paragraph 15. The method according to Paragraph 14, wherein an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is induced in the individual by administering a therapeutically effective amount of a programmed cell death protein 1 (PD-1) ligand.

[0091] Paragraph 16. The method according to Paragraph 15, wherein the PD-1 ligand is programmed death-ligand 1 (PDL-1).

[0092] Paragraph 17. The method according to any one of Paragraphs 10 to 13, wherein the autoimmune disease is AAV or SLE and wherein individual has been identified as one who is at high risk of autoimmune disease progression,

[0093] wherein the treatment comprises treatment with a more frequent or more intense disease treatment regimen, or with a disease regimen not normally administered during the maintenance phase of the autoimmune disease.

[0094] Paragraph 18. The method according to any one of Paragraphs 10 to 13, wherein the autoimmune disease is AAV or SLE and wherein individual has been identified as one who is at low risk of autoimmune disease progression,

[0095] wherein the treatment comprises treatment with a less frequent or less intense disease treatment regimen, or with a disease regimen not normally administered during the maintenance phase of the autoimmune disease.

[0096] Paragraph 19. The method according to any one of Paragraphs 10 to 13, wherein individual has been identified as one who is at high risk of progressing to type 1 diabetes,

[0097] wherein the treatment comprises a prophylactic treatment for type 1 diabetes.

[0098] Paragraph 20. The method according to any one of Paragraphs 10 to 13, wherein the autoimmune disease is IPF and wherein individual has been identified as one who is at high risk of autoimmune disease progression,

[0099] wherein the treatment comprises treatment with nintedanib, pirfenidone, a phosphodiesterase inhibitor, or immunosuppressive therapy.

[0100] Paragraph 21. A programmed cell death protein 1 (PD-1) ligand for use in a method of treating an autoimmune disease in an individual, the method comprising

[0101] (i) determining whether the individual is at high risk of autoimmune disease progression using a method according to any one of Paragraphs 2 to 8, and

[0102] (ii) administering therapeutically effective amount of a PD-1 ligand to the individual if the individual is at high risk of autoimmune disease progression to induce an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in the individual.

[0103] Paragraph 22. A PD-1 ligand for use according to Paragraph 21, wherein the PD-1 ligand is programmed death-ligand 1 (PDL-1).

[0104] Paragraph 23. An in vitro method of assessing whether CD8.sup.+ and CD4.sup.+ T cells in a sample have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising establishing, by determining the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY, whether said phenotype is present,

[0105] wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY relative to the level of expression of these genes in a sample of CD8.sup.+ and CD4.sup.+ T cells which do not have said phenotype.

[0106] Paragraph 24. The method according to any one of Paragraphs 2 to 5, 7, 10 to 16, or 19, wherein the autoimmune disease is type 1 diabetes, and wherein the individual is genetically predisposed to type 1 diabetes.

[0107] Paragraph 25. The method according to Paragraph 24, wherein the individual is a child.

[0108] Paragraph 26. The method according to any one of Paragraphs 24 to 25, wherein the individual has a HLA genotype which is associated with a high risk of type 1 diabetes.

[0109] Paragraph 27. The method according to any one of Paragraphs 24 to 26, wherein the individual has a mother, father and/or sibling with type 1 diabetes.

[0110] Paragraph 28. The method according to any one of Paragraphs 24 to 27, wherein the individual does not have autoantibodies associated with type 1 diabetes.

[0111] Paragraph 29. A method of assessing whether an individual with a chronic infection is at high risk or low risk of progression of said chronic infection, the method comprising:

[0112] (i) determining whether the individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype using the method of Paragraph 1,

[0113] wherein the presence of said phenotype indicates that the individual is at high risk of progression of said chronic infection, and

[0114] wherein the absence of said phenotype indicates that the individual is at low risk of progression of said chronic infection.

[0115] Paragraph 30. A method of assessing whether an individual with a chronic infection is at high risk or low risk of progression of said chronic infection, by determining whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising:

[0116] (i) providing a PBMC sample obtained from the individual;

[0117] (ii) extracting mRNA from the PBMC sample;

[0118] (iii) performing reverse transcription quantitative PCR (RT-qPCR) to convert the mRNA into cDNA and determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0119] wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype, and

[0120] wherein the presence of said phenotype indicates that the individual is at high risk of progression of said chronic infection, and

[0121] wherein the absence of said phenotype indicates that the individual is at low risk of progression of said chronic infection.

[0122] Paragraph 31. A chronic infection progression risk assessment system to determine the risk of an individual with a chronic infection, for use in a method as defined in any one of Paragraphs 29 to 30, the system comprising a tool or tools for determining expression of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY;

[0123] and a computer programmed to compute a risk score of the risk of the individual not responding to the treatment from the gene expression data of the subject.

[0124] Paragraph 32. The method according to any one of Paragraphs 29 to 30, further comprising:

[0125] (ii) selecting an individual identified as one who is at high risk of progression of the chronic infection in step (i) for treatment for said chronic infection.

[0126] Paragraph 33. The method according to any one of Paragraphs 29 to 30, further comprising:

[0127] (ii) subjecting the individual to treatment for the chronic infection if the individual has been identified as one who is at high risk of progression of the chronic infection in step (i).

[0128] Paragraph 34. A method for treating a chronic infection in an individual, the method comprising:

[0129] (i) identifying the individual as one who is at high risk of progression of the chronic infection using a method according to any one of Paragraphs 29 to 30, and

[0130] (ii) subjecting the individual to c treatment for said chronic infection.

[0131] Paragraph 35. A method for treating a chronic infection in an individual, the method comprising:

[0132] (i) requesting a test providing the results of an analysis to determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY, in a sample obtained from the individual,

[0133] wherein downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual has said phenotype, and

[0134] (ii) subjecting the individual to treatment for said chronic infection if the individual has said phenotype.

[0135] Paragraph 36. The method according to any one of Paragraphs 29 to 30, further comprising: (ii) selecting an individual identified as one who is at high risk of progression of the chronic infection in step (i) for treatment,

[0136] wherein the treatment comprises inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual.

[0137] Paragraph 37. The method according to any one of Paragraphs 29 to 30, further comprising:

[0138] (ii) subjecting the individual to treatment if the individual has been identified as one who is at high risk of progression of the chronic infection in step (i),

[0139] wherein the treatment comprises inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual.

[0140] Paragraph 38. A method for treating a chronic infection in an individual, the method comprising:

[0141] (i) identifying the individual as one who is at high risk of progression of the chronic infection using a method according to any one of Paragraphs 29 to 30, and

[0142] (ii) subjecting the individual to treatment if the individual has been identified as one who is at high risk of progression of the chronic infection in step (i),

[0143] wherein the treatment comprises inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual.

[0144] Paragraph 39. A method for treating a chronic infection in an individual, the method comprising:

[0145] (i) requesting a test providing the results of an analysis to determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0146] in a sample obtained from the individual,

[0147] downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual has said phenotype, and

[0148] (ii) subjecting the individual to a treatment for the chronic infection with the treatment if the individual has said phenotype,

[0149] wherein the treatment comprises inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual.

[0150] Paragraph 40. The method according to any one of Paragraphs 36 to 39, wherein a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype is induced in the individual by administering a therapeutically effective amount of an inhibitor of programmed cell death protein 1 (PD-1).

[0151] Paragraph 41. A PD-1 inhibitor for use in a method of treating a chronic infection in an individual, the method comprising

[0152] (i) determining whether the individual is at high risk of progression of the chronic infectionusing a method according to any one of Paragraphs 29 to 30, and

[0153] (ii) administering therapeutically effective amount of a PD-1 ligand to the individual if the individual is at high risk of progression of the chronic infection to induce a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual.

[0154] Paragraph 42. The method according to any one of Paragraphs 29 to 30, 32 to 40, the risk assessment system according to Paragraph 31, or the PD1 inhibitor for use according to Paragraph 41, wherein the chronic infection is a chronic viral infection, a chronic bacterial infection or a chronic parasitic infection.

[0155] Paragraph 43. A method of assessing whether an individual is at high risk or low risk of not mounting an effective immune response to a vaccine against a disease, the individual having received the vaccination, wherein the method comprises:

[0156] (i) determining whether the individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype using the method of Paragraph 1,

[0157] wherein the presence of said phenotype indicates that the individual at high risk of not mounting effective immune response to the vaccination, and

[0158] wherein the absence of said phenotype indicates that the individual is at low risk of not mounting effective immune response to the vaccination.

[0159] Paragraph 44. A method of assessing whether an individual at high risk or low risk of not mounting an effective immune response to a vaccine against a disease, the individual having received the vaccination, by determining whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising:

[0160] (i) providing a PBMC sample obtained from the individual;

[0161] (ii) extracting mRNA from the PBMC sample;

[0162] (iii) performing reverse transcription quantitative PCR (RT-qPCR) to convert the mRNA into cDNA and determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0163] wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype, and

[0164] wherein the presence of said phenotype indicates that the individual at high risk of not mounting effective immune response to the vaccination, and

[0165] wherein the absence of said phenotype indicates that the individual is at low risk of not mounting effective immune response to the vaccination.

[0166] Paragraph 45. A vaccination non-response risk assessment system for use in a method as defined in any one of Paragraphs 43 to 44, the system comprising a tool or tools for determining expression of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY;

[0167] and a computer programmed to compute an vaccination non-response risk score from the gene expression data of the subject.

[0168] Paragraph 46. The method according to any one of Paragraphs 43 to 44, further comprising:

[0169] (ii) selecting an individual identified as one who is at high risk of not mounting an effective immune response to a vaccine in step (i) for vaccination with a further dose of the same vaccine, or with a different vaccine against the same disease.

[0170] Paragraph 47. The method according to any one of Paragraphs 43 to 44, further comprising:

[0171] (ii) subjecting the individual to vaccination with a further dose of the same vaccine, or with a different vaccine against the same disease, if the individual has been identified as one who is at high risk of not mounting an effective immune response to a vaccine in step (i).

[0172] Paragraph 48. A method for vaccinating an individual, the method comprising:

[0173] (i) identifying the individual as one who is at high risk of not mounting an effective immune response to a vaccine using a method according to any one of Paragraphs 43 to 44, and

[0174] (ii) subjecting the individual to vaccination with a further dose of the same vaccine, or with a different vaccine against the same disease.

[0175] Paragraph 49. A method for vaccinating an individual, the method comprising:

[0176] (i) vaccinating the individual;

[0177] (ii) requesting a test providing the results of an analysis to determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY, in a sample obtained from the individual,

[0178] wherein downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual has said phenotype, and

[0179] (iii) subjecting the individual to vaccination with a further dose of the same vaccine, or with a different vaccine against the same disease, if the individual has said phenotype.

[0180] Paragraph 50. The method according to any one of Paragraphs 46 to 49, wherein the individual is subjected to treatment, or selected for subjection to treatment, with a treatment for inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual prior to vaccination of the individual with a further dose of the vaccine.

[0181] Paragraph 51. The method according to Paragraph 50, wherein a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype is induced in the individual by administering a therapeutically effective amount of an inhibitor of programmed cell death protein 1 (PD-1).

[0182] Paragraph 52. A PD-1 inhibitor for use in a method of vaccinating an individual, the method comprising

[0183] (i) determining whether the individual is at high risk of not mounting an effective immune response to a vaccine using a method according to any one of Paragraphs 43 to 44, and

[0184] (ii) administering therapeutically effective amount of a PD-1 ligand to the individual if the individual is at high risk of not mounting an effective immune response to a vaccine to induce a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual;

[0185] (iii) subjecting the individual to vaccination with a further dose of the same vaccine, or with a different vaccine against the same disease.

[0186] Paragraph 53. A method of assessing whether an individual is at high risk or low risk of infection-associated immunopathology, the method comprising:

[0187] (i) determining whether the individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype using the method of Paragraph 1,

[0188] wherein the presence of said phenotype indicates that the individual is at low risk of infection-associated immunopathology, and

[0189] wherein the absence of said phenotype indicates that the individual is at high risk of infection-associated immunopathology.

[0190] Paragraph 54. A method of assessing whether an individual is at low risk or high risk of infection-associated immunopathology, by determining whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising:

[0191] (i) providing a PBMC sample obtained from the individual;

[0192] (ii) extracting mRNA from the PBMC sample;

[0193] (iii) performing reverse transcription quantitative PCR (RT-qPCR) to convert the mRNA into cDNA and determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0194] wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype, and

[0195] wherein the presence of said phenotype indicates that the individual is at low risk of infection-associated immunopathology, and

[0196] wherein the absence of said phenotype indicates that the individual is at high risk of infection-associated immunopathology.

[0197] Paragraph 55. An infection-associated immunopathology risk assessment system for use in a method as defined in any one of Paragraphs 53 to 54, the system comprising a tool or tools for determining expression of two more genes selected from the group consisting of:

[0198] KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY;

[0199] and a computer programmed to compute an infection-associated immunopathology risk score from the gene expression data of the subject.

[0200] Paragraph 56. The method according to any one of Paragraphs 53 to 54, further comprising:

[0201] (ii) selecting an individual identified as one who is at high risk of infection-associated immunopathology in step (i) for treatment for the infection-associated immunopathology.

[0202] Paragraph 57. The method according to any one of Paragraphs 53 to 54, further comprising:

[0203] (ii) subjecting an individual identified as one who is at high risk of infection-associated immunopathology in step (i) to treatment for the infection-associated immunopathology.

[0204] Paragraph 58. A method for treating an infection-associated immunopathology in an individual, the method comprising:

[0205] (i) identifying the individual as one who is at high risk of infection-associated immunopathology using a method according to any one of Paragraph 53 to 54, and

[0206] (ii) subjecting the individual to treatment for the infection-associated immunopathology.

[0207] Paragraph 59. A method for treating an infection-associated immunopathology in an individual, the method comprising:

[0208] (i) requesting a test providing the results of an analysis to determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY, in a sample obtained from the individual,

[0209] wherein upregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and downregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual does not have said phenotype, and

[0210] wherein the absence of said phenotype indicates that the individual is at high risk of infection-associated immunopathology,

[0211] (ii) treating the individual for the infection-associated immunopathology of the individual does not have said phenotype.

[0212] Paragraph 60. The method according to any one of Paragraphs 56 to 59, wherein the treatment comprises inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in the individual.

[0213] Paragraph 61. The method according to Paragraph 60, wherein an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is induced in the individual by administering a therapeutically effective amount of a PD-1 ligand.

[0214] Paragraph 62. The method according to Paragraph 61, wherein the PD-1 ligand is PDL-1.

[0215] Paragraph 63. A PD-1 ligand for use in a method of treating an infection-associated immunopathology in an individual, the method comprising

[0216] (i) determining whether the individual is at high risk of infection-associated immunopathology using a method according to any one of Paragraphs 53 to 54, and

[0217] (ii) administering therapeutically effective amount of a PD-1 ligand to the individual if the individual is at high risk of infection-associated immunopathology to induce an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in the individual.

[0218] Paragraph 64. A PD-1 ligand for use according to Paragraph 63, wherein the PD-1 ligand is PDL-1.

[0219] Paragraph 65. A method of assessing whether an individual is at high risk or low risk of transplant rejection, the method comprising:

[0220] (i) determining whether the individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype using the method of Paragraph 1,

[0221] wherein the presence of said phenotype indicates that the individual is at low risk of transplant rejection, and

[0222] wherein the absence of said phenotype indicates that the individual is at high risk of transplant rejection.

[0223] Paragraph 66. A method of assessing whether an individual is at high risk or low risk of transplant rejection, by determining whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising:

[0224] (i) providing a PBMC sample obtained from the individual;

[0225] (ii) extracting mRNA from the PBMC sample;

[0226] (iii) performing reverse transcription quantitative PCR (RT-qPCR) to convert the mRNA into cDNA and determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0227] wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype, and

[0228] wherein the presence of said phenotype indicates that the individual is at low risk of transplant rejection, and

[0229] wherein the absence of said phenotype indicates that the individual is at high risk of transplant rejection.

[0230] Paragraph 67. A transplant rejection risk assessment system for use in a method as defined in any one of Paragraphs 65 to 66, the system comprising a tool or tools for determining expression of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY;

[0231] and a computer programmed to compute an transplant rejection risk score from the gene expression data of the subject.

[0232] Paragraph 68. The method according to any one of Paragraphs 65 to 66, further comprising:

[0233] (ii) selecting an individual identified as one who is at low risk of transplant rejection in step (i) for organ and/or tissue transplantation.

[0234] Paragraph 69. The method according to any one of Paragraphs 65 to 66, further comprising:

[0235] (ii) subjecting the individual to organ and/or tissue transplantation if the individual has been identified as one who is at low risk of transplant rejection in step (i).

[0236] Paragraph 70. A method for organ and/or tissue transplantation in an individual, the method comprising:

[0237] (i) identifying the individual as one who is at low risk of transplant rejection using a method according to any one of Paragraphs 65 to 66, and

[0238] (ii) subjecting the individual to organ/and or tissue transplantation.

[0239] Paragraph 71. A method for organ and/or tissue transplantation in an individual, the method comprising:

[0240] (i) requesting a test providing the results of an analysis to determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY, in a sample obtained from the individual,

[0241] wherein downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual has said phenotype, and

[0242] (ii) subjecting the individual to organ/and or tissue transplantation if the individual has said phenotype.

[0243] Paragraph 72. The method according to any one of Paragraphs 65 to 66, further comprising:

[0244] (ii) selecting an individual identified as one who is at high risk of transplant rejection in step (i) for treatment prior to organ and/or tissue transplantation, wherein the treatment comprises inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in the individual.

[0245] Paragraph 73. The method according to any one of Paragraphs 65 to 66, further comprising:

[0246] (ii) subjecting the individual to treatment prior to organ and/or tissue transplantation if the individual has been identified as one who is at high risk of transplant rejection in step (i) wherein the treatment comprises inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in the individual.

[0247] Paragraph 74. A method for treating an individual prior to organ and/or tissue transplantation, the method comprising:

[0248] (i) identifying the individual as one who is at high risk of transplant rejection using a method according to any one of Paragraphs 65 to 66, and

[0249] (ii) subjecting the individual to treatment to induce an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in the individual;

[0250] (iii) subjecting the individual to organ/and or tissue transplantation.

[0251] Paragraph 75. A method for treating an individual prior to organ and/or tissue transplantation, the method comprising:

[0252] (i) requesting a test providing the results of an analysis to determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY, in a sample obtained from the individual,

[0253] wherein upregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and downregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual does not have said phenotype, and

[0254] (ii) subjecting the individual to treatment to induce an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in the individual if the individual does not have said phenotype;

[0255] (iii) subjecting the individual to organ/and or tissue transplantation.

[0256] Paragraph 76. The method according to any one of Paragraphs 72 to 75, wherein an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is induced in the individual by administering a therapeutically effective amount of a programmed cell death protein 1 (PD-1) ligand.

[0257] Paragraph 77. A PD-1 ligand for use in a method of treating an individual prior to organ and/or tissue transplantation, the method comprising

[0258] (i) determining whether the individual is at high risk of transplant rejection using a method according to any one of Paragraphs 65 to 66,

[0259] (ii) administering therapeutically effective amount of a PD-1 ligand to the individual if the individual is at high risk of infection-associated immunopathology to induce an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in the individual, and

[0260] (iii) subjecting the individual to organ/and or tissue transplantation.

[0261] Paragraph 78. A PD-1 ligand for use according to Paragraph 77, wherein the PD-1 ligand is PDL-1.

[0262] Paragraph 79. A method of assessing whether an individual is at high risk or low risk of cancer progression, the method comprising:

[0263] (i) determining whether the individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype using the method of Paragraph 1,

[0264] wherein the presence of said phenotype indicates that the individual is at high risk of cancer progression, and

[0265] wherein the absence of said phenotype indicates that the individual is at low risk of cancer progression.

[0266] Paragraph 80. A method of assessing whether an individual is at high risk or low risk of cancer progression, by determining whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising:

[0267] (i) providing a PBMC sample obtained from the individual;

[0268] (ii) extracting mRNA from the PBMC sample;

[0269] (iii) performing reverse transcription quantitative PCR (RT-qPCR) to convert the mRNA into cDNA and determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0270] wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype, and

[0271] wherein the presence of said phenotype indicates that the individual is at high risk of cancer progression, and

[0272] wherein the absence of said phenotype indicates that the individual is at low risk of cancer progression.

[0273] Paragraph 81. A cancer progression risk assessment system for use in a method as defined in any one of Paragraphs 79 to 80, the system comprising a tool or tools for determining expression of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY;

[0274] and a computer programmed to compute an cancer progression risk score from the gene expression data of the subject.

[0275] Paragraph 82. The method according to any one of Paragraphs 79 to 80, further comprising:

[0276] (ii) selecting an individual identified as one who is at high risk of cancer progression in step (i) for treatment for the cancer.

[0277] Paragraph 83. The method according to any one of Paragraphs 79 to 80, further comprising:

[0278] (ii) subjecting the individual to treatment for the cancer if the individual has been identified as one who is at high risk of cancer progression in step (i).

[0279] Paragraph 84. A method for treating cancer in an individual, the method comprising:

[0280] (i) identifying the individual as one who is at high risk of cancer progression using a method according to any one of Paragraphs 79 to 80, and

[0281] (ii) subjecting the individual to treatment for the cancer .

[0282] Paragraph 85. A method for treating cancer in an individual, the method comprising:

[0283] (i) requesting a test providing the results of an analysis to determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0284] in a sample obtained from the individual,

[0285] wherein downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual has said phenotype, and

[0286] (ii) subjecting the individual to treatment for the cancer.

[0287] Paragraph 86. The method according to any one of Paragraphs 82 to 85, wherein the treatment comprises inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual.

[0288] Paragraph 87. The method according to Paragraph 86, wherein a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype is induced in the individual by administering a therapeutically effective amount of an inhibitor of programmed cell death protein 1 (PD-1).

[0289] Paragraph 88. A PD-1 inhibitor for use in a method of treating cancer in an individual, the method comprising

[0290] (i) determining whether the individual is at high risk of cancer progression using a method according to any one of Paragraphs 79 to 80, and

[0291] (ii) administering therapeutically effective amount of a PD-1 ligand to the individual if the individual is at high risk of cancer progression to induce a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual.

[0292] Paragraph 89. A method, risk assessment system, PD-1 ligand for use, or PD-1 inhibitor for use according to any one of the preceding Paragraphs, wherein the sample is a whole blood or peripheral blood mononuclear cell (PBMC) sample.

[0293] Paragraph 90. A method, risk assessment system, PD-1 ligand for use, or PD-1 inhibitor for use according to any one of the preceding Paragraphs wherein the expression level of said two or more genes is determined using reverse transcription quantitative PCR (RT-qPCR).

[0294] Paragraph 91. An in vitro method for identifying a substance capable of inducing an exhausted CD8.sup.+ T cell phenotype in an individual, the method comprising:

[0295] (i) providing a sample of CD8.sup.+ T cells;

[0296] (ii) incubating the CD8.sup.+ T cells in the presence of anti-CD2, anti-CD3 and anti-CD28 antibodies, IL2, and in the presence or absence of a substance of interest; and

[0297] (iii) determining the expression level of IL7R and PD-1 by the CD8.sup.+ T cells;

[0298] wherein a lower expression of IL7R and a higher expression of PD-1 by the CD8.sup.+ T cells in the presence of the substance of interest than in the absence of the substance of interest indicates that the substance is capable of inducing an exhausted CD8.sup.+ T cell phenotype in an individual.

[0299] Paragraph 92. An in vitro method for identifying a substance capable of inducing a non-exhausted CD8.sup.+ T cell phenotype in an individual, the method comprising:

[0300] (i) providing a sample of CD8.sup.+ T cells;

[0301] (ii) incubating the CD8.sup.+ T cells in the presence of anti-CD3 and anti-CD28 antibodies, IL2, and in the presence or absence of a substance of interest; and

[0302] (iii) determining the expression level of IL7R and PD-1 by the CD8.sup.+ T cells;

[0303] wherein a higher expression of IL7R and a lower expression of PD-1 by the CD8.sup.+ T cells in the presence of the substance of interest than in the absence of the substance of interest indicates that the substance is capable of inducing a non-exhausted CD8.sup.+ T cell phenotype in an individual.

[0304] Paragraph 93. The method according to Paragraph 91 or 92, wherein the method further comprises formulating a substance identified as capable of inducing an exhausted CD8.sup.+ T cell phenotype in an individual, or capable of inducing a non-exhausted CD8.sup.+ T cell phenotype in an individual, into a medicament.

[0305] Paragraph 94. A method of preparing CD8.sup.+ T cells with a non-exhausted CD8.sup.+ T cell phenotype, the method comprising:

[0306] (i) providing a sample of CD8.sup.+ T cells obtained from an individual;

[0307] (ii) incubating the CD8.sup.+ T cells in the presence of anti-CD2, anti-CD3 and anti-CD28 antibodies, and IL2; and

[0308] (iii) determining the expression level of IL7R and PD-1 by the CD8.sup.+ T cells;

[0309] wherein a higher expression of IL7R and a lower expression of PD-1 by the CD8.sup.+ T cells following incubation in the presence of the anti-CD2, anti-CD3 and anti-CD28 antibodies, and IL2 compared with prior to incubation, indicates that the CD8.sup.+ T cells have a non-exhausted CD8.sup.+ T cell phenotype.

[0310] Paragraph 95. A method of preparing CD8.sup.+ T cells with an exhausted CD8.sup.+ T cell phenotype, the method comprising:

[0311] (i) providing a sample of CD8.sup.+ T cells obtained from an individual;

[0312] (ii) incubating the CD8.sup.+ T cells in the presence of anti-CD3 and anti-CD28 antibodies, and IL2; and

[0313] (iii) determining the expression level of IL7R and PD-1 CD8.sup.+ T cells;

[0314] wherein a lower expression of IL7R and a higher expression of PD-1 by the CD8.sup.+ T cells following incubation in the presence of the anti-CD3 and anti-CD28 antibodies, and IL2 compared with prior to incubation, indicates that the CD8.sup.+ T cells have an exhausted CD8.sup.+ T cell phenotype.

[0315] Paragraph 96. The method according to Paragraph 94 or 95, wherein said method further comprises administering the CD8.sup.+ T cells to the individual from which the CD8.sup.+ T cells were obtained.

[0316] Paragraph 97. A kit for assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, or whether an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is present in a sample of CD8.sup.+ and CD4.sup.+ T cells, wherein said kit comprises reagents for establishing the expression level of two or more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY.

BRIEF DESCRIPTION OF THE FIGURES

[0317] FIG. 1: T cell costimulation with CD2 prevents development of an exhausted IL7R.sup.loPD1.sup.hi phenotype. (A) Schematic of the magnetic bead system providing variable TCR signal duration/costimulation during in vitro culture. (B-D) Linear plots showing IL7R.sup.hi population resulting from (B) 36 h (top line [at endpoint]) v 6 d (bottom line [at endpoint]) anti-CD3/28 stimulation, (C) 6 d anti-CD2/3/28 (top line) v 6 d anti-CD3/28 (bottom line) and (D) from 6 d anti-CD2/3/28 with (bottom line) and without (top line) Fc-PDL1.

[0318] FIG. 2: A surrogate marker of CD4.sup.+ T cell costimulation/lack of CD8.sup.+ T cell exhaustion in PBMC gene expression data correlates with clinical outcome in chronic viral infection, vaccination, infection and autoimmunity. (A) Scatterplot showing the top 100 genes ranked by ability to identify CD4 T cell costimulation subgroups in PBMC data. x-axis=variable importance. (B) Kaplan-Meier plots showing censored flare-free survival stratified by expression of KAT2B (above or below median) in AAV and SLE patients (n=37, training set) replicated on Affymetrix GeneST1.0 and in an independent cohort (test set, n=47), P=log-rank test. (C) Line and scatterplots showing serial KAT2B expression (n=54) following therapy of chronic HCV infection giving a marked (n=28) or poor response (n=26). P=2-way ANOVA. (D) Boxplot showing post-vaccine malaria protection in a clinical trial (n=43) stratified by KAT2B expression (above or below median), P=Fisher's exact test. (E) Boxplot showing % protection (black) in vaccinees (n=28) following seasonal influenza vaccine stratified by KAT2B expression, P=Fisher's exact test (F) Scatterplot showing neutralizing antibody titer following YF-17D vaccination (yellow fever vaccination), stratified by KAT2B expression (F, above or below median). P=Mann-Whitney test. (G) Line and scatterplot showing serial KAT2B expression throughout dengue infection (n=78) stratified by progression to hemorrhagic fever (DHF, n=24) or uncomplicated course (UD, n=54). x-axis=time (days) relative to defervescence. (H) Boxplot showing % IPF patients (n=75) progressing to transplantation/death (black) stratified by KAT2B expression (above or below median). P=Fisher's exact test. (I-K) Scatterplots showing serial KAT2B expression in healthy age, sex and HLA-matched controls (I) and in pre-T1D cases (n=5), 2 of which seroconvert to islet-cell antibodies (J, black line) and 3 of which develop T1D (K, black line).

[0319] FIG. 3: Top PBMC surrogate markers reflect expression of CD4.sup.+ T cell costimulation/CD8.sup.+ T cell exhaustion modules within CD4.sup.+ T cell and CD8.sup.+ T cell data respectively. Top PBMC-level predictors (n=13) were selected as indicated in FIG. 4A and data is shown comparing expression of the optimal predictor (KAT2B, A, D) and of each other top predictor gene (C, F) in PBMC data compared to expression of the CD4 costimulation module eigengene in CD4 data (A-C) and the CD8 exhaustion signature eigengene in CD8 data (D-F) for n=44 patients with AAV. Significance of correlation, *P<0.05, **P<0.01, ***P<0.001. (B, E) Scatterplots showing the outcome of multiple linear regression models testing the association of KAT2B expression in CD4 (B) and CD8 (F) data (dot at top right of figures) directly compared to clinical markers of disease activity (other dots). x-axis=magnitude of association (regression coefficient, change in normalized flare rate (flares/days follow-up) per unit change in each variable tested). y-axis=significance of association in multiple regression model, P. significance threshold (dashed line, P=0.05). Clinical variables incorporated=disease activity score (BVAS), CRP, Lymphocyte count, neutrophil count, IgG. As expected, surrogate markers showed stronger correlation with the CD4 than the CD8 signature as the algorithm was trained to detect the CD4 costimulation module.

[0320] FIG. 4: Hierarchical clustering of multiple datasets using 13 top PBMC-level surrogate markers of an exhausted CD8.sup.+ T cell/lack of CD4.sup.+ T cell costimulation phenotype identifies patient subgroups with distinct clinical outcomes. Replication of association between surrogate markers of an exhausted CD8.sup.+ T cell/lack of CD4.sup.+ T cell costimulation phenotype signatures and clinical outcome (as shown in FIG. 2C-K) but using all top 13 PBMC-level surrogates rather than KAT2B alone. Clinical outcome associated with each subgroup identified is shown in A (HCV, % responders to IFNa/ribavirin therapy), B (% showing protection versus no protection from malaria vaccine), C (% response to influenza vaccination), D (yellow fever antibody-titer post-vaccination), E (% progression to dengue hemhorrhagic fever, DHF), F (% of idiopathic pulmonary fibrosis patients progressing to need for transplantation or death) and G (% samples from patients with prior or subsequent progression to islet-cell antibody seroconversion or to a diagnosis of T1D). Groups 1 and 2 in FIG. 4 refer to individuals with a non-exhausted CD8+ T cell/CD4+ T cell costimulation phenotype, and to individuals with an exhausted CD8+ T cell/lack of CD4+ T cell costimulation phenotype, respectively.

[0321] Further aspects and embodiments of the invention will be apparent to those skilled in the art given the present disclosure including the following experimental exemplification.

[0322] "and/or" where used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. For example "A and/or B" is to be taken as specific disclosure of each of (i) A, (ii) B and (iii) A and B, just as if each is set out individually herein.

[0323] Unless context dictates otherwise, the descriptions and definitions of the features set out above are not limited to any particular aspect or embodiment of the invention and apply equally to all aspects and embodiments which are described.

[0324] Certain aspects and embodiments of the invention will now be illustrated by way of example and with reference to the figures described above.

DETAILED DESCRIPTION OF THE INVENTION

[0325] The present inventors have identified a gene expression signature that can be used to identify an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in a sample comprising CD8.sup.+ and CD4.sup.+ T cells, such as a PBMC or whole blood sample. Specifically, the present inventors have discovered that an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY. The GenBank accession numbers and version numbers for these genes are set out in Table 1. The present inventors have also discovered that an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is indicative of whether an individual is:

[0326] at low risk of: autoimmune disease progression, infection-associated immunopathology, or transplant rejection; and

[0327] at high risk of: chronic infection progression or not responding to a treatment for a chronic infection, not mounting an effective immune response to a vaccine, or cancer progression.

[0328] A method disclosed herein, such as a method of assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, or whether CD8.sup.+ and CD4.sup.+ T cells in a sample have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, or identifying a substance capable of inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in an individual, may comprising determining the expression level of two more genes selected from the group consisting of KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, KERA and VCY. Determining the expression level of two or more of said genes is expected to be more robust than determining the expression level of only a single gene, such as KAT2B alone. For example, determining the expression level of two or more genes may allow the presence, or absence, of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype to be accurately determined even if the expression level of e.g. one gene cannot be determined, or is inaccurate. Genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, PDE4D, KERA, and VCY represent the top 13 marker genes for determining the presence, or absence, of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, as identified by the present inventors.

[0329] For example, a method disclosed herein, may comprise determining the expression level of three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, eleven or more, twelve or more, or all thirteen genes selected from the group consisting of KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, KERA and VCY. Preferably, a method disclosed herein comprises determining the expression level of KAT2B and one or more genes selected from the group consisting of CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, KERA and VCY. For example, a method disclosed herein may comprise determining the expression level of KAT2B and two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, eleven or more, or all twelve genes selected from the group consisting of CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, KERA and VCY.

[0330] Exhausted CD8.sup.+ T Cell or Lack of CD4.sup.+ T Cell Costimulation Phenotypes

[0331] An individual who has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype has downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY compared with an individual who does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype. An upregulated or downregulated expression of a gene preferably refers to a significantly upregulated, or significantly downregulated, level of expression of said gene, respectively. An individual who does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, may also be referred to as an individual who has a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype. Whether an individual has an upregulated or downregulated level of expression of the genes in question may be determined by any convenient means and many suitable techniques are known in the art and described herein.

[0332] As is the case with most biomarkers, accuracy of prediction may not be absolute. An individual who is at high risk of autoimmune disease progression, progression of a chronic infection, not responding to a treatment for a chronic infection, not mounting an effective immune response to vaccination, infection-associated immunopathology, transplant rejection, or cancer progression, may therefore have a 50% or greater, 60% or greater, 70% or greater, 80% or greater, or 90% or greater chance of autoimmune disease progression, cancer progression, progression of a chronic infection, not responding to a treatment for a chronic infection, not mounting an effective immune response to vaccination, or transplant rejection than an individual who does not have a high risk CD8.sup.+ T cell/CD4.sup.+ T cell phenotype. Similarly an individual who is at low risk of autoimmune disease progression, cancer progression, progression of a chronic infection, not responding to a treatment for a chronic infection, not mounting an effective immune response to vaccination, or transplant rejection may have a 55% or lower, 50% or lower, 40% or lower, 30% or lower, 20% or lower, or 10% or lower chance of autoimmune disease progression, cancer progression, progression of a chronic infection, not responding to a treatment for a chronic infection, not mounting an effective immune response to vaccination, or transplant rejection than an individual who has a high risk CD8.sup.+ T cell/CD4.sup.+ T cell phenotype.

[0333] There are many suitable methods which may be used to determine whether an individual, or cell sample, has upregulated or downregulated expression of two or more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, KERA, and VCY.

[0334] For example, the level of expression of two or more genes selected from the group consisting of KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, PDE4D, KERA and VCY in a sample, which may be a sample obtained from an individual, (i.e. the test sample) may be compared with a threshold level for each gene in question. A threshold level for a gene can be determined using qPCR expression data and network modelling (for example using support vector machines, principal component or adaptive elastic net approaches) to establish optimal expression thresholds that allow maximal, optimal separation of our existing cohorts into discrete prognostic subgroups. Comparison of the level of expression of two or more genes selected from the group consisting of KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, PDE4D, KERA and VCY with threshold levels for the genes in question may indicate whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype.

[0335] Alternatively, the control may be the median expression of the genes in question (i.e. two or more genes selected from the group consisting of KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, PDE4D, KERA and VCY) in samples obtained from a group of individuals, wherein the group comprised individuals, preferably at least 100, at least 50, or at least 10 individuals, who did not have autoimmune disease progression, did not have progression of a chronic infection, did not respond to a treatment for a chronic infection, did not mount an effective immune response to vaccination, did not develop infection-associated immunopathology, did not experience transplant rejection, or had cancer progression, as applicable. In this case, an equal or below median expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, or PDE4D, or an equal or above median expression level of genes KERA or VCY in a sample may indicate the presence of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, while an above median expression genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, or PDE4D, or below median expression level of genes KERA or VCY in a sample may indicate the absence of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype.

[0336] As a further alternative, the control may the median expression of the genes in question in samples obtained from a group of individuals, preferably at least 100, at least 50, or at least 10 individuals, wherein the group comprised individuals who had autoimmune disease progression, did not have progression of a chronic infection, responded to a treatment for a chronic infection, mounted an effective immune response to a vaccine, developed infection-associated immunopathology, experienced transplant rejection, or did not experience cancer progression, as applicable. In this case, a below median expression level of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, or PDE4D, or an above median expression level of genes KERA or VCY in a sample may indicate the presence of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, while an equal or above median expression level of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, or PDE4D, or an equal or below median expression level of genes KERA or VCY in a sample may indicate the absence of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype.

[0337] As a yet further alternative, the control may be the median expression of the genes in question in samples obtained from a group of individuals, preferably at least 100, at least 50, or at least 10 individuals, wherein the group comprised individuals who did and did not have autoimmune disease progression, did and did not have cancer progression, did and did not have progression of a chronic infection, did and did not respond to treatment for a chronic infection, did and did not mount an effective immune response to vaccination, did and did not develop infection-associated immunopathology, or did and did not experience transplant rejection, as applicable. Preferably the group comprised an equal number, or essentially equal number, of individuals who did and did not have autoimmune disease progression, cancer progression, progression of a chronic infection, respond to a treatment for a chronic infection, mount an effective immune response to vaccination, develop infection-associated immunopathology, or experience transplant rejection, as applicable. In this case, a below median expression level of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, or PDE4D, or above median expression level of genes KERA or VCY in a sample may indicate the presence of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, while an above median expression level of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, or PDE4D, or below median expression level of genes KERA or VCY in a sample may indicate the absence of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype.

[0338] In the case of type 1 diabetes the control sample may have been obtained from an individual who did not progress to type 1 diabetes. The control sample may have been obtained from an individual who did not develop type 1 diabetes-associated autoantibodies. Preferably, the control sample was obtained from an individual with the same genetic predisposition to type 1 diabetes as the individual from which the test sample was obtained. Most preferably, the control sample was obtained from an individual with the same high risk HLA haplotype, as the individual from which the test sample was obtained. The control sample may have been obtained from an individual with no first degree relatives with type 1 diabetes. Preferably, the individuals in the group were the same age, as the individual from which the test sample was obtained.

[0339] Determining Gene Expression

[0340] The level of expression of genes KAT2B, CASK, ABCD2, DLG 1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, KERA and VCY may be determined by any convenient means and many suitable techniques are known in the art. For example, suitable techniques include: reverse-transcription quantitative PCR (RT-qPCR), microarray analysis, enzyme-linked immunosorbent assays (ELISA), protein chips, flow cytometry (such as Flow-FISH for RNA, also referred to as FlowRNA), mass spectrometry, Western blotting, and northern blotting. A method of the invention may therefore comprise bringing a sample obtained from an individual into contact with a reagent suitable for determining the expression level of KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, KERA and/or VCY, e.g. a reagent or reagents suitable for determining the expression level of one or more of said genes using RT-qPCR, microarray analysis, ELISA, protein chips, flow cytometry, mass spectrometry, or Western blotting. For example, the reagent may be a pair or pairs of nucleic acid primers, suitable for determining the expression level of one or more of said genes using RT-qPCR. Alternatively, the reagent may be an antibody suitable for determining the expression level of said one or more genes using ELISA or Western blotting. Preferably, the level of expression of said genes is determined using RT-qPCR or Flow-FISH. More preferably, the level of expression of said genes is determined using RT-qPCR.

[0341] RT-qPCR allows amplification and simultaneous quantification of a target DNA molecule. To analyze gene expression levels using RT-qPCR, the total mRNA of a PBMC or whole blood sample may first be isolated and reverse transcribed into cDNA using reverse transcriptase. For example, mRNA levels can be determined using e.g. Taqman Gene Expression Assays (Applied Biosystems) on an ABI PRISM 7900HT instrument according to the manufacturer's instructions. Transcript abundance can then be calculated by comparison to a standard curve.

[0342] Flow-FISH for RNA employs flow cytometry to determine the abundance of a target mRNA within a sample using fluorescently-tagged RNA oligos. This technique is described, for example, in Porichis et al., Nat Comm (2014) 5:5641. The advantage of this technique is that it can be used without the need to separate the cells present in a sample.

[0343] Microarrays allow gene expression in two samples to be compared. Total RNA is first isolated from, e.g. PBMCs or whole blood using, for example, Trizol or an RNeasy mini kit (Qiagen). The isolated total RNA is then reverse transcribed into double-stranded cDNA using reverse transcriptase and polyT primers and labelled using e.g. Cy3- or Cy5-dCTP. Appropriate Cy3- and Cy5-labelled samples are then pooled and hybridised to custom spotted oligonucleotide microarrays comprised of probes representing suitable genes and control features, such as the microarray described in (Willcocks et al., J Exp Med 205, 1573-82, 2008). Samples may be hybridised in duplicate, using a dye-swap strategy, against a common reference RNA derived from pooled PBMC or whole blood samples. Following hybridisation, arrays are washed and scanned on e.g. an Agilent G2565B scanner. Suitable alternatives to the steps described above are well known in the art and would be apparent to the skilled person. The raw microarray data obtained can then be analyzed using suitable methods to determine the relative expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, KERA and VCY.

[0344] Enzyme-linked immunosorbent assays (ELISAs) allow the relative amounts of proteins present in a sample to be detected. The sample is first immobilized on a solid support, such as a polystyrene microtiter plate, either directly or via an antibody specific for the protein of interest. After immobilization, the antigen is detected using an antibody specific for the target protein. Either the primary antibody used to detect the target protein may be labelled to allow detection, or the primary antibody can be detected using a suitably labelled secondary antibody. For example, the antibody may be labelled by conjugating the antibody to a reporter enzyme. In this case, the plate developed by adding a suitable enzymatic substrate to produce a visible signal. The intensity of the signal is dependent on the amount of target protein present in the sample.

[0345] Protein chips, also referred to as protein arrays or protein microarrays, allow the relative amounts of proteins present in a sample to be detected. Different capture molecules may be affixed to the chip. Examples include antibodies, antigens, enzymatic substrates, nucleotides and other proteins. Protein chips can also contain molecules that bind to a range of proteins. Protein chips are well known in the art and many different protein chips are commercially available.

[0346] Western blotting also allows the relative amounts of proteins present in a sample to be detected. The proteins present in a sample are first separated using gel electrophoresis. The proteins are then transferred to a membrane, e.g. a nitrocellulose or PVDF membrane, and detected using monoclonal or polyclonal antibodies specific to the target protein. Many different antibodies are commercially available and methods for making antibodies to a given target protein are also well established in the art. To allow detection, the antibodies specific for the protein(s) of interest, or suitable secondary antibodies, may, for example, be linked to a reporter enzyme, which drives a colorimetric reaction and produces a colour when exposed to an appropriate substrate. Other reporter enzymes include horseradish peroxidase, which produces chemiluminescence when provided with an appropriate substrate. Antibodies may also be labelled with suitable radioactive or fluorescent labels. Depending on the label used, protein levels may be determined using densitometry, spectrophotometry, photographic film, X-ray film, or a photosensor.

[0347] Flow cytometry allows the relative amounts of proteins present in e.g. a PBMC or whole blood sample obtained from a subject to be determined. Flow cytometry can also be used to detect or measure the level of expression of a protein of interest on the surface of cells. Detection of proteins and cells using flow cytometry normally involves first attaching a fluorescent label to the protein or cell of interest. The fluorescent label may for example be a fluorescently-labeled antibody specific for the protein or cell of interest. Many different antibodies are commercially available and methods for making antibodies specific for a protein of interest are also well established in the art.

[0348] Mass spectrometry, e.g. matrix-assisted laser desorption/ionization (MALDI) mass spectrometry, allows the identification of proteins present in a sample obtained from a individual using e.g. peptide mass finger printing. Prior to mass spectrometry the proteins present in the sample may be isolated using gel electrophoresis, e.g. SDS-PAGE, size exclusion chromatography, or two-dimensional gel electrophoresis.

[0349] In the methods described herein, the expression level of two or more genes selected from the group consisting of KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, KERA and VCY may be determined in an individual, e.g. in a sample obtained from an individual, to assess whether the individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype.

[0350] Kit of Parts

[0351] Also disclosed is a kit for use in assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, or whether an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is present in a sample comprising CD8.sup.+ and/or CD4.sup.+ T cells. The kit comprises reagents for establishing the expression level of two or more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY. The GenBank accession numbers and version numbers for these genes are set out in Table 1. The kit may comprise reagents for establishing the expression level of three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, eleven or more, twelve or more, or all thirteen of the genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY. Preferably, the kit comprises reagents for establishing the expression level of KAT2B, along with reagents for establishing the expression level of one or more, two or more, three or more, four or more, five or more, six or more, seven or more, eight or more, nine or more, ten or more, eleven or more, or all 12 genes selected from the group consisting of CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY.

[0352] The reagents may be reagents suitable for establishing the expression KAT2B using RT-qPCR, microarray analysis, ELISA, and/or western blotting. For example, the kit may comprise primers suitable for establishing the level of expression of KAT2B, using e.g. RT-qPCR. The design of suitable primers is routine and well within the capabilities of the skilled person. In addition to detection reagents, a kit may include one or more articles and/or reagents for performance of the method, such as buffer solutions, and/or means for obtaining the test sample itself, e.g. means for obtaining and/or isolating a sample and sample handling containers (such components generally being sterile). The kit may include instructions for use of the kit in a method for assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, or whether an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is present in a sample of CD8.sup.+ and CD4.sup.+ T cells.

[0353] Sample

[0354] One advantage of the genes whose expression is determined in the present invention is that expression of these genes can be determined in unseparated peripheral blood mononuclear cells (PBMCs) or whole blood. Thus, a sample, as referred to in the context of the present invention may be a PBMC or whole blood sample.

[0355] Individual

[0356] "Individual" refers to a human individual. An individual may also be referred to as a patient, i.e. a human patient.

[0357] Autoimmune Disease

[0358] Autoimmune disease is common, affecting about 10% of the population. Management of autoimmune diseases usually involves immunosuppressive therapy which, although often effective, can result in infection which is a significant cause of morbidity and mortality associated with these diseases. Many autoimmune diseases present with an initial acute phase followed by sporadic relapses rather than a continuous disease progression. Treatment usually involves an initial period of intensive treatment, referred to as induction therapy, during the first presentation of the disease followed by maintenance therapy, which is aimed at preventing relapses. However, disease progression varies widely between individuals, ranging from those that have frequent relapses after the initial acute phase to those which have no relapses at all.

[0359] Given the substantive morbidity and mortality associated with immunosuppressive therapy, it would be advantageous if patients unlikely to have relapses of the disease in question could be identified. Identification of these patients would allow clinicians to reduce the immunosuppressive maintenance therapy for these individuals, or even stop it completely, with a corresponding decrease in the morbidity and mortality associated with this form of treatment. In addition, individuals likely to have frequent relapses may benefit from a more intensive form of maintenance therapy, which would not be justified if given to all patients indiscriminately due to the severity of the likely side effects.

[0360] Although many autoimmune diseases present with heterogeneous clinical features in the clinic, it is not possible, on the basis of these clinical features, to determine what the likely pattern of disease progression for a given patient will be, and a number of tests have been developed with a view to addressing this problem. For example, in the case of the autoimmune disease anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis, two autoimmune antibodies, one directed against proteinase-3 (PR-3), the other against myeloperoxidase (MPO), have been identified. However, although statistically the presence of anti-proteinase 3 antibodies is associated with disease progression, the association is not sufficiently strong to allow treatment decisions to be made based on the detection of these antibodies. In the case of SLE, the titre of anti-double stranded DNA antibodies has been used to predict disease progression. However, again the association of these antibodies with disease progression is not sufficiently strong to determine therapy. In addition, the present inventors have previously described a method of predicting autoimmune disease flare on the basis of biomarkers as described in WO2010/084312.

[0361] However, there remains a need in the art for accurate methods of predicting disease progression in autoimmune diseases in order to avoid excess morbidity and mortality as a result of unnecessary immunosuppressive therapy.

[0362] The present inventors have discovered that upregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and downregulated expression of genes KERA and VCY, relative to a control indicates that an individual does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype. Furthermore, the absence of this phenotype in an individual indicates that the individual is at high risk of autoimmune disease progression, while the presence of this phenotype in an individual is at low risk of autoimmune disease progression.

[0363] The risk of progression has important implications for the optimal management of the autoimmune disease in these individuals. For the individuals with this phenotype, any benefits of immunosuppressive maintenance therapy may not outweigh the associated increase in morbidity and mortality. In contrast, individuals without this phenotype are likely to benefit substantially from immunosuppressive maintenance therapy, and the benefits are likely to outweigh the risks. In addition, individuals without this phenotype may benefit from more intensive treatment than is usual during the maintenance phase but which would not be justified if given to all individuals indiscriminately due to the severity of the likely side effects of such treatment.

[0364] "Autoimmune disease" refers to any condition which involves an overactive immune response of the body against substances and tissues normally present in the body. The autoimmune disease is preferably an autoimmune disease wherein the presence of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual is at low risk of autoimmune disease progression and wherein the absence of said phenotype is at high risk of autoimmune disease progression. Autoimmune diseases of particular interest include type 1 diabetes, idiopathic pulmonary fibrosis (IPF), systemic lupus erythematosus (SLE), and vasculitis, such as ANCA-associated vasculitis (AAV). The autoimmune disease is preferably not rheumatoid arthritis (RA) or inflammatory bowel disease (IBD).

[0365] "Autoimmune disease progression" refers to the progression of the autoimmune disease after initial presentation of the disease in an individual. For example, autoimmune disease progression may refer to relapses, or flares, of the autoimmune disease experienced by the individual after initial presentation of the autoimmune disease. A relapse or flare may be an event that requires increased therapy, e.g. increased immunosuppressive therapy or surgery. SLE and AAV are characterised by relapses and flares. A high risk of autoimmune disease progression may accordingly refer to a high risk that the individual will experience relapses or flares of the disease after initial presentation, while a low risk of autoimmune disease progression may refer to a low risk that the individual will experience relapses or flares of the disease after initial presentation. Autoimmune disease progression may also refer to an ongoing worsening of clinical features, which can occur in the absence of discrete flares. In the case of IPF, ongoing worsening of clinical features may result in lung transplantation or death. An ongoing worsening of clinical features in the case of IPF may refer to an ongoing reduction in lung function. Methods for measuring lung function are known in the art and include spirometry (principally FVC), TLCO, A-a gradient and transitional dyspnoea index, effort tolerance, hospitalisation indices, imaging (e.g. chest X ray, high resolution CT scan (HRCT) and FDG-PET scanning), and invasive assessments (e.g. bronchoalveolar lavage and lung biopsy). A high risk of autoimmune disease progression may accordingly refer to a high risk that the individual will experience an ongoing worsening of clinical features after initial presentation, while a low risk of autoimmune disease progression may refer to a low risk that the individual will experience an ongoing worsening of clinical features after initial presentation.

[0366] Autoimmune disease progression may also refer to progression to overt disease, such as in the case of type 1 diabetes. A high risk of autoimmune disease progression may accordingly refer to a high risk that the individual will progress to overt disease, while a low risk of autoimmune disease progression may refer to a low risk that the individual will progress to overt disease. Autoimmune disease progression may also refer to an event requiring increased therapy in the form of either increased immunosuppression or surgery. Such events included relapses, or flares, of the disease after a period of remission, as well as instances where the disease does not enter remission in response to initial therapy and increased immunosuppression or surgery is required as a result. A high risk of autoimmune disease progression may accordingly refer to a high risk that the individual will experience events requiring increased therapy after initial presentation of the disease, while a low risk of autoimmune disease progression may refer to a low risk that the individual will experience events requiring increased therapy after initial presentation of the disease.

[0367] Type 1 diabetes, also known as diabetes mellitus type 1 or juvenile diabetes, is an autoimmune disease caused by selective destruction of insulin-producing .beta. cells in the islets of Langerhans (Elo et al., 2010, J Autoimmun. 35, 70-76). The incidence rate varies by geographic region, with 8-17 cases per 100,000 in Northern Europe and the US and 1-3 case per 100,000 in China and Japan. A particularly high incidence rate is seen in Scandinavian countries, with 35 cases per 100,000. Incidence rates are increasing, especially in the Western world (Elo et al., 2010), and it is estimated that 11-22 million individuals worldwide are currently living with type 1 diabetes.

[0368] Type 1 diabetes is usually treated with lifelong insulin replacement therapy, accompanied by dietary management and monitoring of glucose levels. Serious complications of type 1 diabetes are common, especially where the disease is poorly managed. These include heart disease, strokes, nerve damage, retinopathy, kidney disease and kidney failure, as well as miscarriage and stillbirth in pregnant women with diabetes. Occasionally, pancreas transplants are used to cure diabetes but as this requires lifelong immunosuppressive therapy, which is more dangerous than insulin replacement therapy, this is normally only a viable option for individuals also requiring kidney transplants due to kidney failure. Other therapeutic approaches which are being trialed include islet cell transplantation and stem cell educator therapies. However, at present there is no practicable cure for type 1 diabetes.

[0369] There is therefore a need for strategies for preventing the development of type 1 diabetes in high-risk individuals (Elo et al., 2010). This requires identifying individuals at high risk of developing the disease before the onset of the disease. Several genetic risk factors for type 1 diabetes are known. These include high-risk HLA haplotypes, such as DRB1*0401, DRB1*0402, DRB1*0405, DQA*0301, DQB1*0302 and DQB1*0201. A first degree relative with type 1 diabetes also increases the risk of a child developing type 1 diabetes. However, while all of these risk factors increase the risk of an individual developing the disease, they are, in the majority of cases, not sufficiently predictive to allow individuals with a given risk factor or risk factors to be subjected to preventative therapy indiscriminately. For example, the risk of a child developing type 1 diabetes is about 10% if the father or a sibling has type 1 diabetes and about 1-4% if the mother has type 1 diabetes.

[0370] Hence, there is a need for biomarkers which can be used to predict whether an individual, who is genetically predisposed to developing type 1 diabetes, will develop type 1 diabetes prior to the onset of the disease. This would provide a window for treating these individuals with preventative therapy.

[0371] Progression to clinical type 1 diabetes can be monitored by the appearance of autoantibodies against e.g. islet cells (ICA), insulin (IAA), protein tyrosine phosphatase-related IA-2 protein (IA-2A), glutamic decarboxylase (GADA), and cation efflux transporter ZnT8, which are considered to signify the initiation of autoimmunity (Elo et al., 2010). However, it would be advantageous to identify individuals who will progress to type 1 diabetes even before the initiation of autoimmunity. Furthermore, detection of autoantibodies is, in most cases, not 100% predictive of the individual progressing to type 1 diabetes, nor does it indicate how soon onset of the disease will occur.

[0372] There therefore remains a need in the art for methods that allow the identification of individuals who will develop type 1 diabetes prior to the appearance of autoantibodies, as well as biomarkers for predicting likelihood of progression to clinical type 1 diabetes in individuals with detectable autoantibodies.

[0373] The present inventors have discovered that the presence or absence of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in an individual genetically predisposed to type 1 diabetes is indicative of whether the individual is at low or high risk of progressing to type 1 diabetes, respectively.

[0374] Thus, provided herein are methods which may be used to assess whether and individual who is genetically predisposed to type 1 diabetes is at high risk or at low risk of progressing to type 1 diabetes.

[0375] An individual who is genetically predisposed to type 1 diabetes may have a high-risk HLA (human leukocyte antigen) haplotypes type. Such haplotypes are disclosed in Erlich et al., Diabetes (2008) 57:1084, and include DRB1*0301-DQA1*0501-DQB1*0201 (OR 3.64), DRB1*0405-DQA1*0301-DQB1*0302 (OR 11.37), DRB1*0401-DQA1*0301-DQB1*0302 (OR 8.39), DRB1*0402-DQA1*0301-DQB1*0302 (OR 3.63), DRB1*0404-DQA1*0301-DQB1*0302 (OR 1.59), and DRB1*0801-DQB1*0401-DQB1*0402 (OR 1.25). Preferably, the individual has a haplotype comprising DQB1*02 and DQB1*0302.

[0376] In addition, or alternatively, an individual who is genetically predisposed to type 1 diabetes may have first degree relative, i.e. a mother, father, or sibling, who has type 1 diabetes.

[0377] Although type 1 diabetes is frequently considered to be a disease that begins in childhood, it can occur at any age. Approximately 50% of individuals develop the disorder before the age 40. An individual who is genetically predisposed to type 1 diabetes may therefore be any age. For example, an individual who is genetically predisposed to type 1 diabetes may be a child. In this case, the individual may be less than 10, less than 9, less than 8, less than 7, less than 6, less than 5, less than 4, less than 3, less than 2, or less than 1 year in age.

[0378] The present inventors have discovered that the presence or absence of an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in a sample obtained from an individual genetically predisposed to type 1 diabetes, which is indicative of whether the individual is at low risk or high risk of progressing to type 1 diabetes, respectively, can be detected before the individual develops autoantibodies associated with type 1 diabetes. An individual who is genetically predisposed to type 1 diabetes therefore preferably does not have autoantibodies associated with type 1 diabetes. Autoantibodies associated with type 1 diabetes include autoantibodies against islet cells (islet cell antibody; ICA), insulin (insulin autoantibodies; IAA), protein tyrosine phosphatase-related IA-2 protein (islet antigen-2 antibody; IA-2A), glutamic decarboxylase 65 (Glutamic Acid Decarboxylase 65 Autoantibodies; GADA), and/or cation efflux transporter ZnT8 (cation efflux transporter ZnT8 antibody; ZnT8A).

[0379] Progression to type 1 diabetes may refer to the development, or onset of, type 1 diabetes.

[0380] An individual who has, has progressed to, or has developed type 1 diabetes (also referred to as a "progressor") may show one or more symptoms associated with type 1 diabetes. For example, the individual may have autoantibodies against islet cells (islet cell antibody; ICA), insulin (insulin autoantibodies; IAA), protein tyrosine phosphatase-related IA-2 protein (islet antigen-2 antibody; IA-2A), glutamic decarboxylase 65 (Glutamic Acid Decarboxylase 65 Autoantibodies; GADA), and/or cation efflux transporter ZnT8 (cation efflux transporter ZnT8 antibody; ZnT8A). In addition, or alternatively, the individual may a fasting plasma glucose level of 126 mg/dL (7 mmol/L) or higher, a plasma glucose level of 200 mg/dL (11.1 mmol/L) or higher two hours after administration of a 75 g oral glucose load (glucose tolerance test), and/or a glycated hemoglobin level of 6.5 percent or higher.

[0381] An individual who does not have, has not progressed to, or has not developed type 1 diabetes (also referred to as a "non-progressor") may show no symptoms associated with type 1 diabetes. For example, the individual may not have autoantibodies against islet cells (islet cell antibody; ICA), insulin (insulin autoantibodies; IAA), protein tyrosine phosphatase-related IA-2 protein (islet antigen-2 antibody; IA-2A), glutamic decarboxylase 65 (Glutamic Acid Decarboxylase 65 Autoantibodies; GADA), and/or cation efflux transporter ZnT8 (cation efflux transporter ZnT8 antibody; ZnT8A). In addition, or alternatively, the individual may a fasting plasma glucose level of less than 100 mg/dL (5.6 mmol/L), a plasma glucose level of less than 200 mg/dL (11.1 mmol/L) two hours after administration of a 75 g oral glucose load (glucose tolerance test), and/or a glycated hemoglobin level of less than 6.5 percent.

[0382] As explained above, to determine whether an individual, who is genetically predisposed to type 1 diabetes, has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, and hence is at low risk or high risk of progressing to type 1 diabetes, respectively, the level of expression of two or more genes selected from the group consisting of KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, PDE4D, KERA and VCY in a sample, which may be a sample obtained from the individual, (i.e. the test sample) may be compared with control as explained above.

[0383] Where the control is the median expression of two or more genes selected from the group consisting of KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, PDE4D, KERA and VCY in a group of individuals comprising (1) individuals who progressed to type 1 diabetes, (2) individuals who did not progress to type 1 diabetes, or (3) comprised both individuals who progressed to type 1 diabetes and individuals who did not progress to type 1 diabetes, the individuals in said group preferably had the same genetic predisposition to type 1 diabetes as the individual from which the test sample was obtained. Most preferably, the individuals in said group had same high risk HLA haplotype, as the individual from which the test sample was obtained. Preferably, the individuals in the group were the same age, as the individual from which the test sample was obtained.

[0384] As an alternative, in the case of type 1 diabetes, the control may be a standard curve of expression of two or more genes selected from the group consisting of KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, PDE4D, KERA and VCY, derived from samples obtained from a group of individuals who progressed to type 1 diabetes over time. An equal or higher level of expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and an equal or lower level of expression of genes KERA and VCY in a sample obtained from an individual genetically predisposed to type 1 diabetes, compared with the level of expression of these genes shown in the standard curve, at the same time point (age), may indicate that the individual, does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, and hence is at high risk of progression to type 1 diabetes. Conversely, a lower level of expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and a higher level of expression of genes KERA and VCY in a sample obtained from an individual genetically predisposed to type 1 diabetes, compared with the level of expression shown in the standard curve at the same time point (age), may indicate that the individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, and hence is at low risk of progressing to type 1 diabetes.

[0385] Chronic Infection

[0386] There are many infectious diseases that are known to cause chronic infections in humans. The causative agents of such diseases include viruses, bacteria and parasites, such as protozoa. Some individuals are capable of clearing chronic infections without treatment, while in others chronic infection progresses. Progression in this context may refer to continuation of the chronic infection, i.e. the individual continues to have the chronic infection, and/or the development of additional disease. For example, in the case of hepatitis C virus (HCV), some individuals develop cirrhosis and/or hepatocellular carcinoma as a result of chronic HCV infection. Predicting the risk of progression in the case of chronic infections has important implications, as treatment of individuals who are at low risk of progression could be avoided. This would be particularly advantageous where treatment is costly or associated with deleterious side effects. Similarly, individuals who are at low risk of progression could be treated, or selected for treatment, for the chronic infection. There thus remains a need in the art for assessing whether an individual with a chronic infection is at high risk or low risk of not progression of said chronic infection.

[0387] In addition, although treatments for many chronic infections are known, not all individuals respond to treatment, with the result that some individuals treated experience no, or no significant, benefit as a result of the treatment. This presents a problem, especially where treatment is costly and/or associated with deleterious side effects. There therefore remains a need in the art for methods for determining whether an individual is likely to ultimately respond to a treatment for a chronic infection.

[0388] The present inventors have discovered that downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to a control indicates that an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype. Furthermore, the presence of this phenotype in an individual having a chronic infection, who has been subjected to a treatment for the chronic infection, indicates that the individual is at high risk of not responding to the treatment. It is also expected that the presence of this phenotype in an individual having a chronic infection indicates that the individual is at high risk of progression of the chronic infection.

[0389] The present invention thus provides a method of assessing whether an individual with a chronic infection is at high risk or low risk of progression of said chronic infection, as set out in the claims.

[0390] As briefly mentioned above, progression in this context may refer to continuation of the chronic infection, i.e. the individual continues to have the chronic infection, a worsening of the chronic infection, such as the development or worsening of one or more clinical symptoms associated with the chronic infection, and/or the development of additional disease resulting from the chronic infection.

[0391] In addition, the present invention provides a method of assessing whether an individual with a chronic infection is at high risk or low risk of not responding to a treatment for the chronic infection, wherein the individual has been subjected to the treatment, the method comprising:

[0392] (i) determining whether the individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype using the method of claim 1,

[0393] wherein the presence of said phenotype indicates that the individual is at high risk of not responding to the treatment, and

[0394] wherein the absence of said phenotype indicates that the individual is at low risk of not responding to the treatment.

[0395] A method of assessing whether an individual with a chronic infection is at high risk or low risk of not responding to a treatment for the chronic infection, wherein the individual has been subjected to the treatment, by determining whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising:

[0396] (i) providing a PBMC sample obtained from the individual;

[0397] (ii) extracting mRNA from the PBMC sample;

[0398] (iii) performing reverse transcription quantitative PCR (RT-qPCR) to convert the mRNA into cDNA and determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0399] wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype, and

[0400] wherein the presence of said phenotype indicates that the individual is at high risk of not responding to the treatment, and

[0401] wherein the absence of said phenotype indicates that the individual is at low risk of not responding to the treatment, is also provided

[0402] Further provided is a risk assessment system to determine the risk of an individual with a chronic infection not responding to a treatment for the chronic infection, wherein the individual has been subjected to the treatment, for use in a method as described herein, the system comprising a tool or tools for determining expression of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY;

[0403] and a computer programmed to compute a risk score of the risk of the individual not responding to the treatment from the gene expression data of the subject.

[0404] The method may further comprise (ii) selecting an individual identified as one who is at low risk of not responding to the treatment in step (i) for continued treatment with said treatment; or (ii) subjecting the individual to continued treatment with said treatment if the individual has been identified as one who is at low risk of not responding to the treatment in step (i). Alternatively, the method may comprise, (ii) selecting an individual identified as one who is at high risk of not responding to the treatment in step (i) for treatment; or (ii) subjecting the individual to treatment if the individual has been identified as one who is at high risk of not responding to the treatment in step (i); wherein the treatment comprises inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual. A non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype may be induced in an individual by administering a therapeutically effective amount of an inhibitor of programmed cell death protein 1 (PD-1), e.g. as described herein.

[0405] The present invention also provides a method for treating a chronic infection in an individual, wherein the individual has been subjected to a treatment for the chronic infection, the method comprising:

[0406] (i) identifying the individual as one who is at low risk of not responding to the treatment using a method as disclosed herein, and

[0407] (ii) subjecting the individual to continued treatment with the treatment.

[0408] A method for treating a chronic infection in an individual, wherein the individual has been subjected to a treatment for the chronic infection is also provided. This method may comprise:

[0409] (i) requesting a test providing the results of an analysis to determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY, in a sample obtained from the individual,

[0410] wherein downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual has said phenotype, and

[0411] (ii) subjecting the individual to continued treatment with the treatment if the individual does not have said phenotype.

[0412] Further provided is a method for treating a chronic infection in an individual, wherein the individual has been subjected to a treatment for the chronic infection, the method comprising:

[0413] (i) identifying the individual as one who is at high risk of not responding to the treatment using a method as disclosed herein, and

[0414] (ii) subjecting the individual to treatment if the individual has been identified as one who is at high risk of not responding to the treatment in step (i),

[0415] wherein the treatment comprises inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual.

[0416] A method for treating a chronic infection in an individual, wherein the individual has been subjected to a treatment for the chronic infection, the method comprising:

[0417] (i) requesting a test providing the results of an analysis to determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY,

[0418] in a sample obtained from the individual,

[0419] downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype indicates that the individual has said phenotype, and

[0420] (ii) subjecting the individual to continued treatment with the treatment if the individual has said phenotype,

[0421] wherein the treatment comprises inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual, is also provided.

[0422] A further embodiment provides a PD-1 inhibitor for use in a method of treating a chronic infection in an individual, wherein the individual has been subjected to a treatment for the chronic infection, the method comprising

[0423] (i) determining whether the individual is at high risk of not responding to the treatment using a method as described herein, and

[0424] (ii) administering therapeutically effective amount of a PD-1 ligand to the individual if the individual is at high risk not responding to the treatment to induce a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype in the individual.

[0425] An individual who is responsive to a treatment (i.e. a responder) may, in response to said treatment, show an improvement in one or more symptoms associated with the chronic infection. For example, in the case of HCV, the level of one or more biomarkers associated with HCV infection, such as HCV RNA levels, as determined e.g. in a PBMC sample isolated from the individual, may be reduced or eliminated in response to the treatment in an individual who is responsive to said treatment. For example, HCV RNA levels may be reduced by >3.5 log.sub.10 IU/ml in an individual who is responsive to the treatment. A individual who is responsive to a treatment may refer to an individual who shows an improvement in one or more symptoms associated by with the chronic infection by the end of said treatment, e.g. when the treatment cycle is complete. Thus, an individual who is responsive to treatment may refer to an individual who will ultimately respond to the treatment.

[0426] Similarly, an individual who is not responsive to a treatment (i.e. a non-responder) may, in response to said treatment, show no improvement in one or more symptoms associated with the chronic infection. For example, in the case of HCV, the level of one or more biomarkers associated with HCV infection, such as HCV RNA levels, as determined e.g. in a PBMC sample isolated from the individual, may remain the same or not be significantly reduced in response to the treatment in an individual who is not responsive to said treatment. For example, HCV RNA levels may be reduced by <1.5 log.sub.10 IU/ml in an individual who is not responsive to the treatment. A individual who is not responsive to a treatment may refer to an individual who shows no improvement in one or more symptoms associated with the chronic infection by the end of said treatment, e.g. when the treatment cycle is complete. Thus, an individual who is not responsive to treatment may refer to an individual who will not ultimately respond to the treatment.

[0427] As is the case with most treatments, response to treatment may not be absolute. For example, where the individual has a chronic HCV infection, an individual who is at low risk of not respond to a treatment may have a 80% or greater probability of responding to the treatment and an individual who is at high risk of not responding to treatment may have a 54% or lower probability of responding to the treatment. In the case of chronic HCV infection, the treatment may be treatment with ribavirin and pegylated interferon-alpha.

[0428] A chronic infection, as referred to herein, may be a chronic viral infection, a chronic bacterial infection or a chronic parasitic infection. The chronic infection may be chronic hepatitis C (HCV) or chronic Hepatitis B (HBV) infection.

[0429] Vaccination

[0430] For any given vaccine there are some individuals who do not respond to said vaccine, i.e. mount an effective immune response to the vaccine. Identifying individuals who are at high risk of not responding to a vaccine is important as it allows, for example, such individuals to be subjected to booster vaccination, or monitored for subsequent infection and treated where necessary. There therefore remains a need in the art for methods for determining whether an individual is at high risk of not responding to a vaccine.

[0431] The present inventors have discovered that downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to a control indicates that an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype. Furthermore, the presence of this phenotype in an individual who has received a vaccine indicates that the individual is at high risk of not mounting an effective immune response to the vaccine.

[0432] An individual who has mounted an effective immune response to a vaccine may have antibodies against said vaccine. Antibodies against the vaccine in the individual may, for example, be increase relative to a baseline. Methods for measuring antibodies to a particular vaccine are known in the art and include ELISA, for example. In the case of an influenza vaccine, antibodies against the vaccine may be measured using a haemagglutination-inhibition assay. Alternatively, an individual who has mounted an effective immune response to a vaccine may have complete or partial protection from the disease against which the vaccine was directed. For example, an individual who has mounted an effective immune response to an influenza A vaccination may have complete or partial protection from subsequent influenza caused by a strain against which the vaccine was directed.

[0433] Similarly, an individual who has not mounted an effective immune response to a vaccine may not have antibodies against said vaccine, or may not have protection from the disease against which the vaccine was directed. For example, an individual who has not mounted an effective immune response to an influenza vaccine may not have protection from influenza caused by the strain against which the vaccine was directed.

[0434] An individual who has been identified as being at high risk of not mounting an effective immune response to a vaccine against a disease may be subjected to vaccination with, or selected for vaccination with, a further dose of the same vaccine, or a different vaccine against the same disease. A further dose of the vaccine may be identical to a first dose administered to the individual or may be different. For example, the further dose may be an increased dose compared with a first dose administered. Where the individual is subjected to vaccination with, or selected for vaccination with, a different vaccine against the same disease, said vaccine may be capable of eliciting an immune response to a different disease-associated antigen compared with a first vaccine administered to the individual. Alternatively, or additionally, the vaccine may comprise a different adjuvant and/or increased amount of adjuvant, compared with a first vaccine or first vaccine dose administered to the individual.

[0435] Alternatively, an individual who has been identified as being at high risk of not mounting an effective immune response to a vaccine against a disease may be subjected to a prophylactic treatment for the disease against which the vaccine was directed, or selected for treatment with such a prophylactic treatment. A prophylactic treatment may refer to a preventive treatment. For example, an individual who has been identified as being at high risk of not mounting an effective immune response to a malaria vaccine may be subjected to treatment with an antimalarial or selected for treatment with an antimalarial. Prophylactic and preventive treatments for many diseases are known in the art but may be less-preferred than vaccination due to e.g. side effects, in the case of certain types of antimalarial medication.

[0436] As further alternative, an individual who has been identified as being at high risk of not mounting an effective immune response to a vaccine may be subjected to passive vaccination for the disease against which the vaccine was directed, or selected for treatment with such a passive vaccine. Passive vaccination involves the transfer of antibodies against the disease in question to an individual in need thereof. The antibodies may be derived from donor individuals or produced in vitro, such as monoclonal antibodies. Immunity derived from passive vaccination usually lasts a few weeks or months and it thus is generally less preferred than "active" vaccination but may be useful where there is a high risk that the individual will not mounting an effective immune response to a vaccine which has been administered.

[0437] A vaccine, as referred to herein, may be a vaccine for a viral, bacterial or parasitic infection. Parasitic infections, include protozoal infections, such as malaria. The vaccine may be a vaccine against influenza virus, in particular influenza A virus, yellow fever virus, or malaria.

[0438] Infection-Associated Immunopathology

[0439] Some diseases give rise to an excessive inflammatory response in some individuals. For example, infection with dengue virus can result in a wide range of clinical manifestations ranging from asymptomatic infection or self-limiting fever (uncomplicated dengue) to hemorrhagic fever. It is thought that hemorrhagic fever may caused by an excessive inflammatory response to the virus in the individual. Other disease in which an excessive immune response is thought to result in a more severe disease, include influenza virus and Sars coronavirus infections.

[0440] The present inventors have discovered that upregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and downregulated expression of genes KERA and VCY, relative to a control indicates that an individual does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype. The absence of this phenotype in an individual indicates that the individual, in particular an individual suffering from an infection, is at high risk of infection-associated immunopathology.

[0441] The infection-associated immunopathology, as referred to herein, may be any infection in which an individual's immune response to the infection results in tissue damage in the individual. Tissue damage may be manifested as clinical pathology (see for, example, Rouse et al. Nat Rev Immunol 2010; 10:514-26). Many infections causing immunopathology are known in the art. In one example, the infection-associated immunopathology may be the result of dengue haemorrhagic fever. Alternatively, the infection-associated immunopathology may be the result of influenza virus infection (in particular influenza A virus infection), cytomegalovirus (CMV) infection, SARS, Epstein-Barr virus (EBV) infection, Hepatitis A, B, C or E virus infection, coxsackie virus infection, or chikungunya virus infection.

[0442] Transplantation

[0443] Following transplantation, individuals may experience acute rejection, chronic rejection, humoral rejection, or cellular rejection of the transplant. Acute transplant rejection occurs over a period of a few days. Chronic rejection occurs weeks or months after the transplant. Chronic rejection is the most common form of transplant rejection. Given the deleterious effect of transplant rejection, as well as the costs involved, there remains a need in the art for predicting whether an individual is at high or low risk of transplant rejection. Predicting the risk of transplant rejection may also allow for treatment of high risk individuals prior to or following transplantation to reduce the risk of transplant rejection. Transplantation, as referred to herein, is preferably allograft transplantation. Rejection thus preferably refers to allograft rejection.

[0444] The present inventors have discovered that upregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and downregulated expression of genes KERA and VCY, relative to a control indicates that an individual does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype. It is expected that the absence of this phenotype indicates that the individual is at high risk of transplant rejection, in particular acute transplant rejection. An exhausted CD8.sup.+ T cell phenotype is characterised by a reduced proliferative response and impaired cytokine production. This state, and/or the associated state of limited CD4 costimulation, facilitates tolerance of transplanted allografts in the same manner that an exhausted antiviral T cell response facilitates persistence of the pathogen (Thorp et al., Curr Op Org Transplant 2015; 20(1):37-42). By measuring the presence or extent of an exhausted CD8.sup.+ T cell phenotype, the risk of reaching the clinical endpoint of acute (Steger et al. Transplantation 2008; 85(9):1339) or chronic (Sarraj et al. PNAS 2014; 111(33):12145-50) allograft rejection can be determined. An individual at high risk of transplant rejection may be subjected to more frequent and/or more intense monitoring than is usual following transplantation, such that, for example, indications of transplant rejection can be detected and treated earlier when they are more responsive.

[0445] Cancer

[0446] In the case of cancer, progression of the disease differs between different individuals. In some individuals the disease progresses quickly, while in others progression is slow. Given the deleterious side effects of many cancer treatments, as well as the costs involved, there remains a need in the art for predicting whether an individual is at high or low risk of cancer progression.

[0447] The present inventors have discovered that downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to a control indicates that an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype. Furthermore, it is expected that the presence of this phenotype in an individual indicates that the individual is at high risk of cancer progression.

[0448] As mentioned above, assessing whether an individual is at high risk or low risk of cancer progression may be useful in the context of cancer treatment by allowing patients who are likely to benefit from a given treatment to be identified. For example, a given cancer treatment may not show benefit in all patients with a particular cancer but may show benefit in patients at high risk of cancer progression. In addition, or alternatively, a cancer treatment may be associated with side-effects which are too severe for use of the treatment in all patients with a particular cancer but may be acceptable as a treatment for individuals at high risk of cancer progression. Some cancer treatments may similarly be too costly to administer to all patients with a particular cancer but may be justified for treatment of patients at high risk of cancer progression.

[0449] Methods for assessing whether an individual is at high risk or low risk of cancer progression may also be useful in the context of clinical trials as patients at high risk of cancer expression are expected to reach a relevant trial endpoints more quickly or frequently, with the result that a clinical trial involving only individuals assessed to be at high risk of cancer progression will need to include fewer individuals resulting in cost saving, as well as increasing the likelihood of detecting beneficial effect(s) of the treatment being trialled.

[0450] Cancer progression may refer to an increase in the size and/or number of tumours, an increase in organ dysfunction, e.g. as a result of neoplastic infiltration, the emergence or an increase in the number of tumour metastases, a change in the stage or grade of the malignancy, and/or the recurrence of a malignancy after a period of remission, in the individual.

[0451] In Vitro Methods

[0452] To date, it has not been possible to reproduce the phenotype of CD8.sup.+ T cell exhaustion in primary human CD8.sup.+ T cells using in vitro cell culture. The present inventors have discovered that the use of anti-CD2 mediated costimulation in addition to anti-CD3/anti-CD28 mediated T cell activation (FIG. 1) specifically prevents the development of an exhausted CD8.sup.+ T cell phenotype when compared to the use of anti-CD3/anti-CD28 mediated T cell activation alone (FIG. 1 C-D). In this context, CD2-mediated costimulation reproduces the transcriptional signature of CD8.sup.+ T cell exhaustion seen, for example, in autoimmune disease and in chronic infection. However, for purposes of an in vitro assay, it is preferable to measure surrogate markers of a CD8.sup.+ T cell exhaustion phenotype, such as IL7R and PD-1, during T cell proliferation. An exhausted CD8.sup.+ T cell phenotype is characterised by low expression of IL7R and high expression of PD-1, e.g. relative to the level of expression of these genes in an individual who does not have said phenotype, while a non-exhausted CD8.sup.+ T cell phenotype is characterised by high expression of IL7R and low expression of PD-1, e.g. relative to the level of expression of these genes in an individual who does not have said phenotype. Expression of IL7R and PD-1 can be determined by any method known in the art or described herein, such as multi-parameter flow cytometry. Hence, primary human CD8.sup.+ T cells from an individual can be induced to differentiate into CD8.sup.+ T cells with an exhausted CD8.sup.+ T cell phenotype (using anti-CD3/28 antibodies) or into CD8.sup.+ T cells with a non-exhausted CD8.sup.+ T cell (using anti-CD2/3/28 antibodies). Such CD8.sup.+ T cells, as well as the methods to generate such CD8.sup.+ T cells, may find application in different fields, including those described herein.

[0453] Thus, the present invention provides a method of preparing CD8.sup.+ T cells with a non-exhausted CD8.sup.+ T cell phenotype, the method comprising:

[0454] (i) providing a sample of CD8.sup.+ T cells obtained from an individual;

[0455] (ii) incubating the CD8.sup.+ T cells in the presence of anti-CD2, anti-CD3 and anti-CD28 antibodies, and IL2; and

[0456] (iii) determining the expression level of IL7R and PD-1 by the CD8.sup.+ T cells;

[0457] wherein a higher expression of IL7R and a lower expression of PD-1 by the CD8.sup.+ T cells following incubation in the presence of the anti-CD2, anti-CD3 and anti-CD28 antibodies, and IL2 compared with prior to incubation, indicates that the CD8.sup.+ T cells have a non-exhausted CD8.sup.+ T cell phenotype.

[0458] The present invention also provides a method of preparing CD8.sup.+ T cells with an exhausted CD8.sup.+ T cell phenotype, the method comprising:

[0459] (i) providing a sample of CD8.sup.+ T cells obtained from an individual;

[0460] (ii) incubating the CD8.sup.+ T cells in the presence of anti-CD3 and anti-CD28 antibodies, and IL2; and

[0461] (iii) determining the expression level of IL7R and PD-1 CD8.sup.+ T cells;

[0462] wherein a lower expression of IL7R and a higher expression of PD-1 by the CD8.sup.+ T cells following incubation in the presence of the anti-CD3 and anti-CD28 antibodies, and IL2 compared with prior to incubation, indicates that the CD8.sup.+ T cells have an exhausted CD8.sup.+ T cell phenotype. The method may further comprise incubating the CD8.sup.+ T cells in the presence of PDL1, such as an Fc-chimaeric PDL1 protein.

[0463] The method may further comprise administering the CD8.sup.+ T cells to the individual from which the CD8.sup.+ T cells were obtained.

[0464] Adoptive cellular therapy is a method which involves the isolation and transfer of autologous, ex-vivo conditioned immune cells with the aim of modulating an endogenous immune response. Adoptive transfer of activated effector cells has been used with success in cancer (Rosenberg et al. Nat Rev Cancer 2008; 8(4):299-308) and chronic infection (Moss et al. Nat Rev Immunol 2005; 5:9-20) while transfer of thimaeric' T cells specifically transduced with antigen-receptors specific for tumour components (CARs) have also shown promise (Porter et al. NEJM 2011; 365:725-33). Similarly, in autoimmune disease, infection-associated immunopathology, and transplantation, adoptive transfer of T cells with a regulatory phenotype has shown promise in mediating immunoregulation and resolution of disease or organ dysfunction (Riley, J L. Immunity 2009; 30(5):656-65). However, in each instance of adoptive cellular therapy it is essential that the cellular phenotype induced by ex-vivo conditioning creates is characterized by the ability to perform effector/regulatory function and to persist long-term in vivo (Riddell et al. Ann Rev Immunol 1995; 13:545-86). As a T cell undergoes effector differentiation there is a progressive loss of its ability to persist and to carry out its intended in vivo function after adoptive transfer (Gattinoni et al. Nat Rev Immunol 2006; 6:383). Current methods of in vitro differentiation of T cells result in the development of effector function but loss of longevity (Gattinoni et al. Nat Rev Immunol 2006; 6:383). Some methods aim to prevent this endpoint and are being further trialed (Gattinoni et al. Nat Med 2011; 17(10):1290-7). It has been proposed that treatments limiting the development of CD8.sup.+ T cell exhaustion may maximize the longevity and success of adoptive therapy (Kamphorst A O, Immunotherapy 2013; 5(9):975-87) but there has to date been no means by which exhaustion in primary human T cells can be prevented during ex-vivo conditioning. We propose that by providing additional CD2-mediated costimulation during ex-vivo conditioning exhaustion may be usefully prevented prior to adoptive transfer.

[0465] Thus, the present invention provides a method of preparing CD8.sup.+ T cells with a non-exhausted CD8.sup.+ T cell phenotype for autologous cellular therapy, the method comprising:

[0466] (i) providing a sample of CD8.sup.+ T cells obtained from an individual;

[0467] (ii) incubating the CD8.sup.+ T cells in the presence of an anti-CD2 antibody; and

[0468] (iii) determining the expression level of IL7R and PD-1 by the CD8.sup.+ T cells;

[0469] wherein a higher expression of IL7R and a lower expression of PD-1 by the CD8.sup.+ T cells following incubation in the presence of the anti-CD2 antibody compared with prior to incubation, indicates that the CD8.sup.+ T cells have a non-exhausted CD8.sup.+ T cell phenotype. The method may further comprise administering the CD8.sup.+ T cells to the individual from which the CD8.sup.+ T cells were obtained.

[0470] The correlation of CD8.sup.+ T-cell exhaustion with disease outcome has obvious therapeutic implications. The present inventors have shown using an in vitro model that the use of biologic agents to alter CD8.sup.+ T-cell co-stimulation can modify CD8.sup.+ T cell exhaustion. CD8.sup.+ T cell exhaustion may be promoted by enhancing costimulation (using an anti-CD2 antibody) or limited by providing additional coinhibitory signals (by using e.g. an Fc-chimaeric PDL1 protein). The in vitro assay may be used for screening a compound libraries and/or additional coinhibitory or costimulatory molecules for their potential effects on T cell exhaustion. This would facilitate selection of a substance capable of inducing an exhausted CD8.sup.+ T cell phenotype, or a non-exhausted CD8.sup.+ T cell phenotype, in an individual in need thereof, as described elsewhere herein. For example, a substance capable of inducing an exhausted CD8.sup.+ T cell phenotype may be used in the treatment of autoimmune diseases.

[0471] Thus, provides is an in vitro method for identifying a substance capable of inducing an exhausted CD8.sup.+ T cell phenotype in an individual, the method comprising:

[0472] (i) providing a sample of CD8.sup.+ T cells;

[0473] (ii) incubating the CD8.sup.+ T cells in the presence of anti-CD2, anti-CD3 and anti-CD28 antibodies, IL2, and in the presence or absence of a substance of interest; and

[0474] (iii) determining the expression level of IL7R and PD-1 by the CD8.sup.+ T cells;

[0475] wherein a lower expression of IL7R and a higher expression of PD-1 by the CD8.sup.+ T cells in the presence of the substance of interest than in the absence of the substance of interest indicates that the substance is capable of inducing an exhausted CD8.sup.+ T cell phenotype in an individual.

[0476] Also provided is an in vitro method for identifying a substance capable of inducing a non-exhausted CD8.sup.+ T cell phenotype in an individual, the method comprising:

[0477] (i) providing a sample of CD8.sup.+ T cells;

[0478] (ii) incubating the CD8.sup.+ T cells in the presence of anti-CD3 and anti-CD28 antibodies, IL2, and in the presence or absence of a substance of interest; and

[0479] (iii) determining the expression level of IL7R and PD-1 by the CD8.sup.+ T cells;

[0480] wherein a higher expression of IL7Rand a lower expression of PD-1 by the CD8.sup.+ T cells in the presence of the substance of interest than in the absence of the substance of interest indicates that the substance is capable of inducing a non-exhausted CD8.sup.+ T cell phenotype in an individual. The method may further comprise incubating the CD8.sup.+ T cells in the presence of PDL1, such as an Fc-chimaeric PDL1 protein.

[0481] Where a method comprises determining the expression level of IL7R and PD-1 by the CD8.sup.+ T cells, the method may further comprise measuring/determining cell proliferation. Methods for measuring/determining cell proliferation are known in the art and include e.g. CFSE dilution.

[0482] The method may also comprise formulating a substance identified as capable of inducing an exhausted CD8.sup.+ T cell phenotype in an individual, or capable of inducing a non-exhausted CD8.sup.+ T cell phenotype in an individual, into a medicament. Formulation into a medicament may comprise formulating the substance with a suitable pharmaceutical excipient. Suitable excipients are known in the art.

[0483] Treatment

[0484] In the case of autoimmune disease, chronic infection, infection-associated immunopathology and cancer, treatment may refer to therapeutic treatment of ongoing disease intended to manage the disease, treatment to cure the disease, or treatment to provide relief from the symptoms of the disease, as well as prophylactic treatment to prevent disease in an individual at high risk of developing a disease, as applicable.

[0485] In the case of autoimmune disease, chronic infection, infection-associated immunopathology and cancer, treatment may be any known treatment for the disease in question. The application of such known treatments is well within the capabilities of the skilled practitioner.

[0486] Treatment may comprise inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, or inducing a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype, in the individual, as applicable in the context. An exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype may be induced in an individual by administering a therapeutically effective amount of a programmed cell death protein 1 (PD-1) ligand, such as programmed death-ligand 1 (PDL-1). A non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype may be induced in an individual by administering a therapeutically effective amount of an inhibitor of PD-1. PD-1 inhibitors are known in the art and include nivolumab (PD-1 blockade). Alternatively, a non-exhausted CD8.sup.+ T cell or CD4.sup.+ T cell costimulation phenotype may be induced in an individual by administering a therapeutically effective amount of an inhibitor of cytotoxic T-lymphocyte-associated protein 4 (CTLA4). Again, inhibitors of CTLA4 are known in the art and include ipilimumab. Such `checkpoint` blockade of exhaustion-associated inhibitory receptors has proved a successful therapy for some cancer patients (Pardoll, D M. The blockade of immune checkpoints in cancer immunotherapy. Nat Rev Cancer 2012; 12(4):252-64). However, only a minority of patients show a sustained response to this promising therapy. A major focus remains the identification of markers allowing prediction of response to checkpoint therapy and, while some progress has been made (Day et al., Nature 2006; Erbst et al., Nature 2014), no biomarker is sufficiently robust to allow clinical stratification and patient selection. Detection of a CD8.sup.+ T cell exhaustion or lack of CD4.sup.+ T cell costimulation phenotype is expected to allow individuals most likely to benefit from such therapy to be identified.

[0487] Alternatively, treatment may comprise treatment with CD8.sup.+ T cells having an exhausted, or non-exhausted, CD8.sup.+ T cell phenotype, as applicable in the context. CD8.sup.+ T cells with an non-exhausted CD8.sup.+ T cell phenotype are expected to be useful in the treatment of diseases in which a non-exhausted CD8.sup.+ T cell phenotype is beneficial, such as cancer treatment, for example, while CD8.sup.+ T cells with an exhausted CD8.sup.+ T cell phenotype are expected to be useful in the treatment of disease in which an exhausted CD8.sup.+ T cell phenotype is beneficial, such as treatment of autoimmune diseases. Accordingly, an individual at high risk of cancer progression may be treated with CD8.sup.+ T cells which have a non-exhausted CD8.sup.+ T cell phenotype, for example. Methods for preparing CD8.sup.+ T cells having an exhausted, or non-exhausted, CD8.sup.+ T cell phenotype are described herein. In the context of treatment, the CD8.sup.+ T cells are preferably CD8.sup.+ T cells obtained from the individual to be treated which have been induced to exhibit an exhausted, or non-exhausted, CD8.sup.+ T cell phenotype as required by the context.

[0488] Thus, also provided is a plurality of CD8.sup.+ T cells with a non-exhausted CD8.sup.+ T cell phenotype for use in a method of treatment in an individual, the method comprising:

[0489] (i) providing a sample of CD8.sup.+ T cells obtained from the individual;

[0490] (ii) incubating the CD8.sup.+ T cells in the presence of anti-CD2, anti-CD3 and anti-CD28 antibodies, and IL2;

[0491] (iii) determining the expression level of IL7R and PD-1 by the CD8.sup.+ T cells;

[0492] wherein a higher expression of IL7R and a lower expression of PD-1 by the CD8.sup.+ T cells following incubation in the presence of the anti-CD2, anti-CD3 and anti-CD28 antibodies, and IL2, compared with prior to incubation, indicates that the CD8.sup.+ T cells have a non-exhausted CD8.sup.+ T cell phenotype; and

[0493] administering the CD8.sup.+ T cells having a non-exhausted CD8.sup.+ T cell phenotype to the individual.

[0494] Further provided is a plurality of CD8.sup.+ T cells with an exhausted CD8.sup.+ T cell phenotype for use in a method of treatment in an individual, the method comprising:

[0495] (i) providing a sample of CD8.sup.+ T cells obtained from the individual;

[0496] (ii) incubating the CD8.sup.+ T cells in the presence of anti-CD3 and anti-CD28 antibodies, and IL2;

[0497] (iii) determining the expression level of IL7R and PD-1 CD8.sup.+ T cells;

[0498] wherein a lower expression of IL7R and a higher expression of PD-1 by the CD8.sup.+ T cells following incubation in the presence of the anti-CD3 and anti-CD28 antibodies, and IL2, compared with prior to incubation, indicates that the CD8.sup.+ T cells have an exhausted CD8.sup.+ T cell phenotype; and

[0499] administering the CD8.sup.+ T cells having an exhausted CD8.sup.+ T cell phenotype to the individual.

[0500] In the case of autoimmune disease, treatment may comprise selecting for treatment, or treating, an individual identified as one who is at high risk of autoimmune disease progression with a more frequent or more intense disease treatment regimen, or with a disease regimen not normally administered during the maintenance phase of the autoimmune disease. A more frequent or more intense disease treatment regimen may refer to a disease treatment regimen that is more frequent or more intense than the treatment normally administered during the maintenance phase of the autoimmune disease. An example of a more intense disease treatment regimen is intermittent rituximab treatment, e.g. in the case of AAV. Similarly treatment in this context may comprise selecting for treatment, or treating, an identified as one who is at low risk of autoimmune disease progression with a less frequent or less intense disease treatment regimen, or with a disease regimen not normally administered during the maintenance phase of the autoimmune disease. A less frequent or less intense disease treatment regimen may refer to a disease treatment regimen that is less frequent or less intense than the treatment normally administered during the maintenance phase of the autoimmune disease. For example, "treatment" with a less frequent or less intense disease treatment regimen may comprise stopping maintenance therapy for a subject identified as having a low risk phenotype. Alternatively, an individual who has been identified as one who is at high risk of autoimmune disease progression may be selected for treatment, or treated with a prophylactic treatment for the autoimmune disease in question. For example, where an individual is identified as one who is at high risk of progressing to type 1 diabetes the individual may be selected for, and/or subjected to, treatment for type 1 diabetes, such as an early stage treatment or a prophylactic treatment. A prophylactic treatment may refer to a preventive treatment. Individuals identified as being at high risk of IPF progression may be treated, or selected for treatment, with nintedanib, pirfenidone, or a phosphodiesterase inhibitor (e.g. sildafenil). Alternatively, individuals identified as being at high risk of IPF progression may be treated, or selected for treatment, with immunosuppressive therapy, such as treatment with azathioprine, colchicine, cyclophosphamide, cyclosporine, endothelin receptor antagonists, anti-TNF therapy, methotrexate, Interferon gamma-1b or penicillamine. Immunosuppressive therapy is not normally employed as a treatment in IPF but may be beneficial in individuals who are at high risk of IPF progression. As a further alternative, treatment of individuals identified as being at high risk of IPF progression may comprise increased levels of supportive care, such as monitoring, investigation, supplemental oxygen therapy, pulmonary rehabilitation, anticoagulation, or prophylactic vaccination.

[0501] In the case of infection-associated immunopathology, treatment is particularly challenging as it requires the need to balance pathogen-directed immunity, and immunopathology driven by an aggressive immune response, in the individual. Identifying individuals at high risk of infection-associated immunopathology is therefore important, as it allows treatment to be targeted at those most likely to require it without unnecessarily suppressing the immune response in individuals at low risk of infection-associated immunopathology. For example, an individual who is at high risk infection-associated immunopathology may be treated, or selected for treatment, with an immunomodulatory treatment, such as corticoid steroid therapy. Corticoid steroid therapy has been trialled, for example, in the treatment of immunopathology associated with SARS coronavirus infection (Lee et al., NEJM 2003; 348:1986-94) and pneumococcal infection (Damjanovic, D et al. Marked improvement of severe lung immunopathology by influenza-associated pneumococcal superinfection requires both the control of bacterial superinfection and host immune responses. Am J Pathol 2013; 183(3):868-80).

[0502] In the case of chronic HCV infection, treatment may be treatment with ribavirin and pegylated interferon-alpha or a direct-acting anti-viral agent (Liang et al. NEJM 2014, 370:2043-7).

[0503] In the case of transplant rejection, an individual determined to be at high risk of transplant rejection may be treated, or selected for treatment, with a different or more intense immunosuppressive therapy than that normally administered following transplantation.

[0504] Experimental Section

[0505] Materials and Methods

[0506] Patients.

[0507] Ethical approval for this study was obtained from the Cambridge Local Research Ethics Committee (REC reference numbers 04/023, 08/H0306/21,08/H0308/176) and informed consent was obtained from all subjects enrolled.

[0508] AAV Patients

[0509] 59 AAV patients attending or referred to the specialist vasculitis unit at Addenbrooke's hospital, Cambridge, UK between July 2004 and May 2008 were enrolled into the present study. Active disease at presentation was defined by Birmingham vasculitis activity score (BVAS.sup.31) and the clinical impression that induction immunosuppression would be required. Prospective disease monitoring was undertaken monthly with serial BVAS disease scoring.sup.31 and full biochemical, hematological and immunological profiling followed by treatment with an immunosuppressant and tapering dose steroid therapy. At each time-point of follow-up, disease activity was allocated into one of three categories defined as follows:

[0510] 1. Flare (at least 1 major or 3 minor BVAS criteria),

[0511] 2. low grade activity (0 major and 1-2 minor BVAS criteria),

[0512] 3. no activity (0 major or minor BVAS criteria).

[0513] All disease flares were crosschecked against patient records to confirm clinical impression of disease activity and the need for intensified therapy as a result. Disease activity scoring was performed by a single investigator (EFM), blinded to gene expression data at the time of scoring. Additional flares were defined in the absence of BVAS scoring if patients attended for emergency investigation (bronchoscopy, or specialist ophthalmological or Ear/Nose/Throat surgical review) that confirmed evidence of active disease. To differentiate between discrete flares, clear improvement in disease activity was required in the form of an improvement in flare-related symptoms together with a reduction in BVAS score, a reduction in markers of inflammation (CRP, ESR), and a reduction in immunosuppressive therapy.

[0514] SLE Patients

[0515] The SLE cohort was composed of 23 patients attending or referred to the Addenbrooke's Hospital specialist vasculitis unit between July 2004 and May 2008 meeting at least four ACR SLE criteria.sup.32, presenting with active disease (defined below) and in whom immunosuppressive therapy was to be commenced or increased. Following treatment with an immunosuppressant patients were followed up monthly. Disease monitoring was undertaken with serial BILAG disease scoring.sup.33 and full biochemical, hematological and immunological profiling.

[0516] A discrete disease flare required all three of the following prospectively defined criteria:

[0517] 1. new BILAG score A or B in any system

[0518] 2. clinical impression of active disease by the reviewing physician

[0519] 3. the intention to increase in immunosuppressive therapy as a result.

[0520] Additional flares were defined in the absence of BILAG scoring if patients were admitted directly to hospital as emergency cases for increased immunosuppressive therapy. To differentiate between disease flares clear improvement in disease activity was required in the form of diminished flare-related symptoms together with a reduction in both BILAG score and immunosuppressive therapy.

[0521] IBD Patients

[0522] Patients with active CD and UC were recruited from a specialist IBD clinic at Addenbrooke's Hospital, prior to commencing treatment. Diagnosis was made using standard endoscopic, histologic, and radiological criteria.sup.34. Patients who had already received immunomodulators or corticosteroids were excluded. Enrolled patients were managed conventionally using a step-up strategy3.

[0523] Assessment of disease activity was in accordance with national and international guidelines and included consideration of symptoms, clinical signs, and objective measures, including blood tests (C-reactive protein [CRP], erythrocyte sedimentation rate [ESR], hemoglobin concentration, and serum albumin), stool markers (calprotectin), and mucosal assessment (by sigmoidoscopy or colonoscopy) where appropriate. Validated scoring tools were used as another means of assessing disease activity (Harvey-Bradshaw severity index.sup.35 or simple clinical colitis activity index.sup.36 for CD and UC, respectively), although these were not used to guide treatment decisions. All clinicians were blinded to the microarray results.

[0524] For each disease, all patients were not included in all analyses as, for example, comparison of modular network analysis in related cell types required that samples passing QC filtering were available for all cell types for all patients. Our previous publications have shown that the sample sizes used here are adequate to detect reproducible signatures correlating with clinical traits.

[0525] Follow Up Analysis.

[0526] Comparisons of outcome and associated clinical variables between subgroups were analyzed using the Kaplan-Meier log-rank test and non-parametric Mann Whitney U test or the Chi-square test as appropriate. Correction for multiple testing was applied using the Bonferroni method or false discovery rate (FDR, Benjamini and Hochberg method) where appropriate as indicated.

[0527] Cell Separation and RNA Extraction.

[0528] Venepuncture was performed at a similar time of day in all cases to minimize gene expression differences arising from circadian variation.sup.37. Peripheral blood mononuclear cells (PBMC), CD4 and CD8 T cells were isolated from 110 ml of whole blood by centrifugation over ficoll and positive selection using magnetic beads as previously described.sup.20. The purity of separated cell subsets was determined by flow cytometry and included as a covariate in downstream correlation and network analyses. Total RNA was extracted from each cell population using an RNeasy mini kit (Qiagen) with quality assessed using an Agilent BioAnalyser 2100 and RNA quantification performed using a NanoDrop ND-1000 spectrophotometer.

[0529] Microarray Gene Expression Profiling

[0530] HsMediante25k Custom Spotted Microarray

[0531] Total RNA (250 ng) was converted into double-stranded cDNA and labelled with Cy3- or Cy5-dCTP as previously described.sup.20. Appropriate Cy3- and Cy5-labelled samples were pooled and hybridized to custom spotted oligonucleotide microarrays (HsMediante25k) comprised of probes representing 25,342 genes and control features.sup.38. All samples were hybridized in duplicate, using a dye-swap strategy, against a common reference RNA derived from pooled PBMC samples. Following hybridization, arrays were washed and scanned on an Agilent G2565B scanner.

[0532] Affymetrix Human Gene 1.0 ST Microarray

[0533] Aliquots of total RNA (200 ng) were labeled using Ambion WT sense Target labeling kit and hybridized to Human Gene 1.0 or 1.1 ST Arrays (Affymetrix) as described. After washing, arrays were scanned using a GS 3000 or Gene Titan scanner (Affymetrix) as appropriate.

[0534] Published Datasets

[0535] Published datasets were accessed through either NCBI-GEO or ArrayExpress, imported into R using the Bioconductor package GEOquery and analyzed as described. Search criteria incorporated the name of individual diseases and were filtered to human datasets but not by platform used. Studies were only included if they met the following criteria:

[0536] 1. Similar QC filters as applied to the data produced in-house were satisfied (described below).

[0537] 2. Samples were taken at an analogous time-point to those from which the costimulation and exhaustion signatures in autoimmunity were identified. i.e. samples taken during active disease without concurrent immunosuppressive therapy.

[0538] 3. Clinical outcome data was available.

[0539] It was not feasible to build a unified predictive model across all available datasets as they originated from different groups and were performed on mutually incompatible microarray platforms.

[0540] For the HCV data used in FIG. 2C a marked response was defined as an HCV titer decrease >3.5 log 10 iu/ml and a poor response as an HCV titer decrease <1.5 log 10 iu/ml by day 28 after commencing combined therapy with ribavirin and pegylated interferon-alpha. For the Malaria vaccine trial used in FIG. 2D `protection` was defined as delayed or complete protection from subsequent confirmed P.Falciparum infection following standardised exposure (x5 bites) compared to infectivity control subjects. For the influenza data used in FIG. 2E protection was defined as >/=1 high response to at least 1 (of 3) included strains. A high response was defined as >/=4-fold increase in HAI titre at d28 and a titre >/=1:40 as per US FDA guidelines.

[0541] All gene expression data used has been deposited in publicly available repositories (NCBI-GEO and ArrayExpress): AAV, SLE (E-MTAB-2452, E-MTAB-157, E-MTAB-145) IBD (E-MTAB-331), LCMV (GSE9650), HCV (GSE7123), malaria vaccination (GSE18323), influenza vaccination (GSE29619), yellow fever vaccination (GSE13486), dengue fever (GSE25001), IPF (GSE28221), type 1 diabetes (E-TABM-666), NOD (GSE21897), RA (GSE15258, GSE33377), in vitro CD8 stimulation (E-MTAB-3470).

[0542] Data Analysis.

[0543] Preprocessing and Quality Control (QC).

[0544] For Mediante hs25k arrays, raw image data were extracted using Koadarray v2.4 software (Koada Technology) and probes with a confidence score >0.3 in at least one channel were flagged as present. Extracted data were imported into R where log transformation and background subtraction were performed followed by within array print-tip Loess normalization and between-array quantile and scale normalization using the Limma package.sup.39 in Bioconductor.sup.40. Further analysis was then performed in R and only data demonstrating a strong negative correlation (r.sup.2>0.9) between dye swap replicates were used in downstream analyses.

[0545] Affymetrix raw data (.CEL) files were imported into R and subjected to variance stabilization normalization using the VSN package in BioConductor.sup.41. Quality control was performed using the Bioconductor package arrayQualityMetrics.sup.42 with outlying samples removed from downstream analyses. Correction for batch variation was performed using the Bioconductor package ComBat.sup.43 and batch structure was included as a covariate in downstream correlation analyses.

[0546] Clustering.

[0547] Hierarchical clustering was performed using a Pearson correlation distance metric and average linkage analysis, performed either in Cluster with visualization in Treeview.sup.44, using Genepattern.sup.45 or directly in R using hclust in the stats package.

[0548] Differential Expression

[0549] Differentially-expressed genes were identified using linear modeling and an empirical Bayes method.sup.39 using a false discovery rate threshold of 0.05 as indicated to determine significance.

[0550] Weighted Gene Coexpression Network Analysis (WGCNA).

[0551] Highly correlated genes in immune cell subsets were identified and summarized with a modular eigengene profile using the Weighted Gene Coexpression Network Analysis (WGCNA) Bioconductor package in R.sup.46. Normalized, log transformed expression data was variance filtered using the inflexion point of a ranked list of median absolute deviation values for all probes. A soft thresholding power was chosen based on the criterion of approximate scale-free topology.sup.47. Gene networks were constructed and modules identified from the resulting topological overlap matrix with a dissimilarity correlation threshold of 0.01 used to merge module boundaries and a specified minimum module size of n=30. Modules were summarized as a network of modular eigengenes, which were then correlated with a matrix of clinical variables and the resulting correlation matrix visualized as a heatmap. As each module by definition is comprised of highly correlated genes, their combined expression may be usefully summarized by eigengene profiles.sup.48, effectively the first principal component of a given module. A small number of eigengene profiles may therefore effectively `summarize` the principle patterns within the cellular transcriptome with minimal loss of information. This dimensionality-reduction approach also facilitates correlation of ME with clinical traits. Significance of correlation between a given clinical trait and a modular eigengene was assessed using linear regression with Bonferroni adjustment to correct for multiple testing. Independent association of a given module eigengene or gene expression profile (e.g. KAT2B) with clinical outcome was assessed using a multiple linear regression model. Significance of each term in the linear model was plotted against its regression coefficient, as a measure of the strength of association (the regression coefficient reflecting the change in clinical outcome per unit change in modular/gene expression).

[0552] Overlap of signatures with modules derived from network analysis is shown to the right of selected module heatmaps by the following formula to allow correction for variable module size: (signature genes overlapping with module genes, n)/(genes in module, n).times.100. The overlap of randomly selected signatures of equivalent size was used as a control and is shown adjacent to the above plots.

[0553] HOPACH Analysis

[0554] For validation purposes, highly-correlated genes were independently partitioned into discrete modules using a second algorithm, Hierarchical Ordered Partitioning And Collapsing Hybrid (HOPACH.sup.49) in R. This approach differs from WGCNA in that it does not rely on a user-specified correlation threshold to define module boundaries but rather aims to maximize homogeneity of modules. Normalized, log transformed data were clustered using a hierarchical algorithm with modular boundaries defined by the median split silhouette (MSS), a measure of how well-matched a gene is to the other genes within its current cluster versus how well-matched it would be if it were moved to another cluster. On partitioning the dataset into clusters, each cluster is reiteratively subdivided until the MSS is maximized, thereby producing an optimal segregation into maximally discrete modules.

[0555] Knowledge-Based Network Generation and Pathway Analysis

[0556] The biological relevance of gene groups comprising modules identified by co-expression analysis were further investigated using the Ingenuity Pathways Analysis platform.sup.50. Six modules from the CD4 T cell WGCNA analysis showed significant correlation with clinical outcome in AAV after correction for multiple testing (Bonferroni method). The inventors applied network and pathway enrichment analysis to genes comprising these modules to determine whether they may have any biological relevance. Briefly, for network analysis genes from a specified target set of interest are progressively linked together based on a measure of their interconnection, which is derived from described functional interactions. Additional highly interconnected genes that are absent from the target genes (open symbols) may be added to complete a network of arbitrary size (set at n=35). Networks may be ranked by significance which reflects the probability of randomly generating a network of similar size from genes included in the full knowledge database containing at least as many target genes as in the network in question. For pathways analysis, the overrepresentation of canonical pathways (pre-defined, well-characterized metabolic and signaling pathways curated from extensive literature reviews) amongst a specified set of target genes is assessed, with significance determined by computing a Fisher's exact test with false discovery rate correction for multiple testing.

[0557] Gene Set Enrichment Analysis (GSEA)

[0558] GSEA.sup.11 was used to further assess whether specific biological pathways or signatures were significantly enriched between patient subgroups identified by gene modules (as opposed to testing for enrichment of pathways within modules themselves as outlined in the previous section). GSEA determines whether an a priori defined `set` of genes (such as a signature) show statistically significant cumulative changes in gene expression between phenotypic subgroups (such as patients with relapsing or quiescent disease). In brief, all genes are ranked based on their differential expression between two groups then an enrichment score (ES) is calculated for a given gene set based on how often its members appear at the top or bottom of the ranked differential list. 1000 random permutations of the phenotypic subgroups were used to establish a null distribution of ES against which a normalized enrichment score (NES) and FDR-corrected q values were calculated. GSEA was run with a focused subgroup of gene signatures.sup.11 selected to test the null hypothesis that different CD8 T cell phenotypes were not significantly enriched in patient subgroups identified by modular analysis.

[0559] Selection of Optimal PBMC-Level Biomarkers.

[0560] Optimal surrogate markers facilitating identification of the CD4 T cell co-stimulation/CD8 exhaustion signatures in PBMC-level data were determined using a randomforests classification algorithm.sup.51 (FIG. 2A). Although signatures apparent in purified T cell transcriptome data correlate with clinical outcome, they cannot be similarly detected in data derived from PBMC due to the confounding influence of expression from other cell types nor can the same genes be used to predict outcome in PBMC.sup.2,20. However, as CD4 T cell co-stimulation and CD8 T cell exhaustion signatures themselves showed close correlation the inventors hypothesized that this would amplify the signal detectable in PBMC and that detection of the combined CD4/CD8 T cell response may be feasible. The availability of both separated T cell and PBMC data from the same patients at the same time facilitate a supervized search for surrogate markers of the co-stimulation/exhaustion signatures in PBMC. Expression data derived from both CD4 T cells and PBMC were available for a cohort of n=37 patients (AAV and SLE) following QC and hybridization to the HsMediante25k custom microarray platform and constituted a training cohort. Normalized, log-transformed expression data was analyzed using the MLInterfaces Bioconductor package in R.sup.52. Using PBMC-level expression data samples were classified into subgroups showing either high or low expression of the costimluation/exhaustion signature and probes were subsequently ranked using the variable importance metric based on their ability to predict allocation to either group. The variable importance for a given gene reflects the change in accuracy of classification (% increase in MSE or increase in node purity) when that variable is randomly permuted. For a poorly predictive gene, random permutation of its values will minimally influence classification accuracy. Conversely, the most robust predictors will have a comparatively large effect on classification accuracy when randomly permuted. PBMC samples from a subset of n=37 cases derived from the training cohort were labeled and hybridized on an alternative microarray platform (Affymetrix Gene ST1.0) as a technical validation set (FIG. 2B, left panel). PBMC samples from an independent n=47 cases not included in the training cohort were labeled and hybridized to the Affymetrix Gene ST1.0 platform as an independent test set (FIG. 2B, right panel). For both technical validation and independent test sets expression of the optimal biomarker identified in FIG. 2A (KAT2B) was used to bisect the cohort relative to the median expression and clinical outcome was compared in KAT2Bhi and KAT2Blo patients.

[0561] Linear Models

[0562] Linear modeling was performed in R using the stats package. This took the form of fit.rarw.Im(y.about.x1.sup.+ x2.sup.+ x3, data=mydata)

[0563] where y (the response variable) was selected as normalized flare rate (flares/days follow-up) and x.sub.1-x.sub.n (the test variables) were selected to include measures of disease activity (both clinical scores and laboratory markers of inflammation), quantification of circulating leucocyte subsets (lymphocytes, neutrophils) and concurrent measurements of autoantibody titer where relevant. Test variables also included a biomarker profile (e.g. exhaustion signature or KAT2B expression). The significance and magnitude (regression coefficient, reflecting change in response variable (flares/days follow-up) per unit change in each test variable included) were extracted and plotted against each other. Not all clinical or laboratory measures were relevant comparisons in each case and therefore were not all included in every model generated.

[0564] T Cell Culture

[0565] Primary human CD8 T cells were separated from leucocyte cones obtained from NHS Blood and Transplant (Addenbrooke's Hospital, Cambridge, UK) by centrifugation over ficoll and positive selection using magnetic beads as previously described.sup.20. The purity of separated cell subsets was determined by three-color flow cytometry. Purified T cells were labeled with 10 .mu.M CFSE (Invitrogen) and resuspended in complete RPMI 1640 (Sigma Aldrich) in the presence of 10% FCS. Purified CD8.sup.+ T cells (>95%) were then stimulated in sterile, 96-well U-bottomed culture plates (Greiner) using an `artificial APC` consisting of MACS iBead particles (1:2 bead:cell ratio, Miltenyi) or DyneBead particles (Invitrogen) conjugated to either CD3/CD28 or CD2/CD3/CD28 as indicated in the presence of IL2 (10 ng/ml, Gibco life technologies) for 6 days. The magnetic iBead construct was removed after 36 h in some instances as indicated. In some experiments, additional costimulation was provided by the addition of either IFN.alpha. (10 ng/ml, Abcam) or by additional conjugation of recombinant Human PD-L1 Fc Chimera (life technologies, 1 .mu.g/mI) or anti-CD40 antibody (50 ng/ml, Abcam) as indicated. The nature of costimulatory signals tested was based upon the results of the network analysis of CD4 T cell modules described above.

[0566] For restimulation experiments cells were harvested on day 6 post-stimulation and sorted into IL7R.sup.hi and IL7R.sup.lo populations using a FACSAriaIII cell sorter (BD Biosciences) with live/dead discrimination performed using an AquaFluorescent amine-reactive dye (Invitrogen). Cell numbers were normalized and were resuspended in complete RPMI 1640 (2.times.104/ml, Sigma-Aldrich) and `rested` in a sterile, U-bottomed culture plate (Greiner) for 6 days (37.degree. C., 5% CO.sub.2) before being restimulated (anti-CD2/3/28 1:2 bead:cell ratio, Miltenyi MACSiBead) for a further 6 days in the presence of IL2 (10 ng/ml, Gibco life technologies).

[0567] Note that, human memory CD8 T cell subsets do not equivalently respond to the stimulation conditions described above. As primary whole human CD8 T cells are composed of highly variable proportions of memory subsets and whole CD8 T cells were stimulated it was necessary to perform paired tests of significance when comparing resulting T cell subsets and transcriptional profiles.

[0568] Flow Cytometry.

[0569] Immunophenotyping was performed using an LSR Fortessa analyzer (BD Biosciences), and data was analyzed using FlowJo software (Tree Star). Reactions were standardized with multicolor calibration particles (BD Biosciences) with saturating concentrations of the following antibodies: AquaFluorescent Live/Dead (Invitrogen), IL7R.alpha. AF647 (BD biosciences, clone HIL-7R-M21), PDCD1 APC (eBioscience, clone MIH4). For intracellular staining, cells were fixed and permeabilized using a transcription factor staining buffer set (eBioscience) and before staining with saturating concentrations of antibody against BCL2 (BD Biosciences, clone 100).

[0570] Results

[0571] The clinical course of autoimmune and infectious disease varies greatly even between individuals with the same condition. An understanding of the molecular basis for this heterogeneity could lead to significant improvements in both monitoring and treatment ENREF 1. During chronic infection the process of T cell exhaustion inhibits the immune response, facilitating viral persistence.sup.1. The inventors show that a transcriptional signature reflecting CD8 T cell exhaustion is associated with poor clearance of chronic viral infection, but conversely predicts better prognosis in multiple autoimmune diseases. The development of CD8 T cell exhaustion during chronic infection is driven by both persistence of antigen and a lack of accessory `help` signals. In autoimmunity, the inventors found that where evidence of CD4 T cell costimulation was pronounced, that of CD8 T cell exhaustion was reduced.

[0572] The inventors could further reproduce the exhaustion signature by modifying the balance of persistent TCR stimulation and specific CD2-induced costimulation provided to human CD8 T cells in vitro, suggesting that each process plays a role in dictating outcome in autoimmune disease. The "non-exhausted" T cell state driven by CD2-induced costimulation was reduced by signals through the exhaustion-associated inhibitory receptor PD-1, suggesting that induction of exhaustion may be a therapeutic strategy in autoimmune disease and infection-associated immunopathology. Using expression of optimal surrogate markers of costimulation/exhaustion signatures in independent datasets, the inventors confirmed an association with good clinical outcome or response to therapy in infection (hepatitis C virus (HCV)), and vaccination (yellow fever, malaria, influenza) but poor outcome in autoimmune and infection-associated immunopathology (type 1 diabetes (T1D), anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV), systemic lupus erythematosus (SLE), idiopathic pulmonary fibrosis (IPF) and dengue hemorrhagic fever (DHF)). Thus, T cell exhaustion plays a central role in determining outcome in autoimmune disease and targeted manipulation of this process could lead to new therapeutic opportunities.

[0573] In a complex set of data such as the transcriptome, similar measurements may be grouped together by network analysis to form discrete modules ENREF 2 ENREF 3 ENREF 4 that can highlight novel pathways contributing to the pathogenesis of complex diseases ENREF 5. The inventors have previously shown that a CD8 T cell transcriptional signature in patients with multiple immune-mediated diseases can predict a subsequent relapsing disease.sup.2,3. However, the biology underlying this observation was not clear. The inventors therefore applied weighted gene co-expression network analysis.sup.3 to the transcriptomes of purified CD4 and CD8 T cells isolated from a prospective cohort of 44 AAV patients with active, untreated disease.sup.7to further explore the mechanisms driving relapsing autoimmunity. Modules of genes were summarized as `eigengene` profiles that were correlated with clinical variables and visualized in the form of a heatmap. Modules derived from both CD8 and CD4 T cell transcriptomes showed strong correlation with disease outcome but not activity, and were co-correlated despite being mutually exclusive. A similar analysis using a cohort of 23 SLE patients also presenting with active, untreated disease.sup.2 identified analogous CD8 and CD4 T cell expression modules that again correlated with clinical outcome but not disease activity. By contrast a type 1 interferon response signature was associated with disease activity but not with long-term outcome, consistent with previous reports.sup.4.

[0574] Next, the inventors reasoned that genes within co-correlated modules in related cell types might inform the biology of relapsing disease. By selecting CD4 T cell modules showing significant, strong correlation with relapse rate and performing network enrichment analysis the inventors identified a module corresponding to CD4 T cell costimulation. By way of validation the inventors repeated this analysis using an independent co-expression network algorithm that similarly demonstrated association between a CD4 costimulation module and clinical outcome. The independent association of modular signatures with clinical outcome was confirmed using multiple linear regression modeling and was only apparent during active disease.

[0575] During chronic viral infection CD8 T cell memory responses are exquisitely dependent on CD4 T cell costimulation.sup.5,6 which can lead to the resolution of chronic infection in both mice.sup.1 and humans.sup.7. When antigen persists in the absence of costimulation CD8 T cells become `exhausted`.sup.1, a phenotype characterized by progressive loss of effector function, persistent high expression of inhibitory receptors and profound changes in gene expression, distinct from those seen in effector, memory or anergic T cells.sup.8. Although mice lacking inhibitory receptors have an increased incidence and severity of autoimmunity.sup.9,10 a specific role for exhaustion in dictating the outcome of autoimmune responses has not been demonstrated.

[0576] The inventors hypothesized that CD4 T cell signals may be important in limiting exhaustion towards persistent self-antigen during autoreactive immunity, analogous to responses during persistent infection. The inventors therefore used Gene Set Enrichment Analysis (GSEA.sup.11) to test for altered expression of transcriptional signatures reflecting T cell exhaustion (and other T cell-related phenotypes) between patient subgroups defined by the CD8 modular analysis, who go on to develop relapsing or quiescent autoimmunity. Using this approach, the inventors observed that genes specifically downregulated in exhausted CD8 T cells during chronic murine LCMV infection (but not altered in memory, naive or effector cells.sup.8) were similarly downregulated in CD8 T cells from patients at low risk of subsequent relapse.

[0577] During chronic murine LCMV infection, T cell exhaustion is driven by coordinate upregulation of multiple coinhibitory receptors.sup.12 that signal synergistically to produce a state of generalized immunosuppression.sup.13. In autoimmunity, these receptors were not coordinately upregulated as a group. Instead patients with good prognosis from each disease were characterized by upregulation of a distinct subset of exhaustion-associated coinhibitory receptors. Although a divergence from the murine LCMV model, T cell exhaustion accompanied by expression of a limited subset of coinhibitory receptors is similar to that described in intratumoral CD8 T cells.sup.14 which are a target for checkpoint therepy.sup.15,16.

[0578] To confirm whether exhaustion was associated with clinical outcome, the inventors used the murine CD8 T cell exhaustion signature.sup.8 to perform unsupervized hierarchical clustering of three independent cohorts of patients with distinct diseases (AAV, SLE, IBD). In each case this identified a subgroup of patients with both early and recurrent relapses. Whereas CD8 exhaustion was associated with poor outcome in viral infection, in every case it predicted favorable prognosis in autoimmune and infection-associated immunopathology. Again, independent association with outcome was confirmed using multiple linear regression models. Together, these data demonstrate that a transcriptional signature of relative CD8 T cell exhaustion, similar to that determining outcome in chronic viral infection and cancer, is apparent during active, untreated disease in patients with favorable long-term outcome in multiple autoimmune and inflammatory diagnoses.

[0579] CD8 T cell exhaustion is characterized by high expression of coinhibitory receptors (such as PD-1.sup.12) and low expression of nascent memory markers (such as IL7R.sup.17) and is promoted by both the persistence of antigen.sup.18 and a lack of accessory costimulation.sup.6. To understand signals driving exhaustion and outcome in autoimmunity, the inventors attempted to recreate the outcome-associated transcriptional signatures using variable TCR signal duration and costimulation of primary human cells in vitro. The inventors stimulated purified human CD8 T cells using a magnetic bead conjugated with antibodies targeting costimulatory molecules (FIG. 1A) and measured expression of IL7R and PD-1 expression (FIG. 1B-D) as markers indicating an exhausted phenotype. Comparison between persistent (6 days) and transient TCR stimulation (36 hours) showed that IL7R expression returned on a proportion of cells after several divisions when the TCR stimulus was removed but failed to do so if it persisted (FIG. 1B). The inventors then systematically tested whether costimulatory molecules, identified from the CD4 T cell network analysis described above FIGS. 1C-D), could overcome the effect of persistent TCR stimulation during in vitro differentiation. The inventors found that specific costimulation with anti-CD2 (FIG. 1B), but not with other stimuli such as IFN.alpha. or anti-CD40, resulted in maintained IL7R expression, limited upregulation of PD-1 and enhanced cell survival.

[0580] While CD8 exhaustion is known to limit viral control during chronic infection, exhausted cells may be restored to useful function by blocking inhibitory signaling through PD-1.sup.19. Enhancing coinhibitory signals is therefore a logical therapeutic strategy in autoimmune disease, aiming to facilitate exhaustion despite high levels of costimulation that would otherwise be predicted to result in an aggressive relapsing disease course. To test this concept, primary human CD8 T cells were costimulated with anti-CD2 during persistent TCR signaling as above (FIG. 1C) in the presence or absence of a bead-bound Fc-chimeric version of the principal PD-1 ligand, PDL-1 (FIG. 1D). When added to CD2-costimulated CD8 T cell cultures, increased PD-1/PDL-1 signaling suppressed differentiation of a non-exhausted IL7R.sup.hi subpopulation (FIG. 1C-D).

[0581] To define the phenotype of T cell exhaustion more robustly, as small numbers of surface markers are insufficient, the inventors analyzed the transcriptome of CD8 T cells exposed to persistent stimulation with and without CD2 signaling. This CD2 response signature characterized exhausted cells but not effector or memory subsets (by GSEA). Consistent with this, patient clusters generated using the CD2 response signature recreated subgroups similar to those generated using the murine LCMV CD8 exhaustion signature. Thus, CD2 signaling during persistent TCR stimulation of primary human CD8 T cells prevents the development of transcriptional changes characteristic of exhaustion, recreating transcriptional signatures associated with outcome in both viral infection and autoimmunity.

[0582] To confirm that the transcriptional signatures reflected the development of functional exhaustion in vitro, the inventors showed that cells appearing exhausted by surface markers (IL7R.sup.loPD-1.sup.hi) also expressed markers of apoptotic resistance, characteristic cytokine patterns and showed diminished survival on restimulation (BCL2.sup.loIFN.gamma..sup.lo IL10.sup.hi). There was no evidence of preferential accumulation of CD8 T cell subsets following CD2-induced costimulation. These data highlight the importance of CD2 signaling in limiting the development of CD8 T cell exhaustion in the face of persistent TCR simulation, and provide a starting point for more sophisticated attempts to therapeutically exhaust an autoimmune response in a targeted fashion.

[0583] The inventors next aimed to independently validate the association between the balance of CD4 costimulation and CD8 exhaustion with clinical outcome using published datasets. The majority of these profile unseparated peripheral blood mononuclear cells (PBMC), in which T cell-intrinsic signatures are not readily apparent due to the confounding influence of expression from other cell types.sup.20. The inventors therefore used a classification algorithm (randomforests) to identify optimal surrogate markers of costimulation/exhaustion modules in PBMC data from autoimmune patients taken concurrently with the T cells described above (FIG. 2A). As the CD8 exhaustion and CD4 costimulation signatures were themselves correlated, it became easier to detect their combined signal in PBMC using surrogate markers (FIG. 2A, FIG. 3). The top-ranked candidate KAT2B is a transcriptional co-activator known to mediate an anti-apoptotic effect under conditions of metabolic stress.sup.52 and to increase cellular resistance to cytotoxic compounds.sup.53. These characteristics, along with its high expression in memory and T-follicular helper and NK cells, suggest that it may mark the development of a durable, persistent T cell phenotype promoting long-lived responses in either infection or autoimmunity. The observed association was confirmed by both technical replication (using the same samples run on an independent array platform) and independent validation (FIG. 2B).

[0584] ENREF 25 To test whether similar associations may be apparent in multiple infectious and autoimmune diseases the inventors directly compared expression levels of KAT2B (and of the other top surrogate markers, FIG. 4) between clinical subgroups defined within published studies for which PBMC expression and linked clinical outcome data were available. Where subgroups were not pre-specified, the inventors compared clinical outcome in groups stratified as having either above or below-median expression of KAT2B (FIG. 2C-K). Hierarchical clustering using all top surrogate markers gave similar stratification to that seen using KAT2B alone, while as expected the separation of patient subgroups varied slightly in different clinical circumstances (FIG. 2C-K, FIG. 4).

[0585] ENREF 26 ENREF 32 Combined interferon and ribavirin therapy may result in increased virus-specific T cell responses in chronic HCV, although such eradication therapy is successful in only 50% of cases.sup.21 and in some cases no change in endogenous immune response is observed.sup.22. In a cohort of hepatitis C patients receiving combination therapy, KAT2B expression was progressively induced and showed significantly greater induction in patients ultimately responding to therapy (FIG. 2C). In a clinical trial of malaria vaccination.sup.23 high KAT2B expression identified a subgroup with response rates of 78%, almost twice that seen in the low response group (FIG. 2D). Moreover, response to vaccination for either influenza.sup.24 (FIG. 2E) or yellow fever.sup.25 (FIG. 2F) could be predicted by stratifying recipients based on their expression of KAT2B following vaccine exposure. Dengue viral infection can result in a wide range of clinical manifestations ranging from asymptomatic infection or self-limiting fever (uncomplicated dengue, UD) to hemorrhagic fever (DHF). Consistent with our observations in autoimmunity, the inventors observed that KAT2B expression was elevated in patients developing the excessive inflammatory response of DHF (FIG. 2G).sup.26.

[0586] The inventors next asked whether surrogate detection of T cell costimulation/exhaustion modules could predict progression of other autoimmune diseases. Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease characterized by both autoantibodies and autoreactive CD4 T cells.sup.27. In a cohort of 75 IPF patients.sup.28 high expression of KAT2B predicted subsequent progression to transplantation or death (FIG. 2H). The inventors also observed that PBMC Kat2b expression was elevated in the murine NOD model of type 1 diabetes.sup.29 with levels rising sharply during the T cell initiation phase, long before the onset of diabetic hyperglycemia ENREF 43. In a cohort of samples taken prospectively from children at high risk of disease but prior to its onset.sup.30 expression of KAT2B was seen to specifically and progressively rise (FIG. 2I-K) both in patients who progressed to type 1 diabetes and in those who developed islet-cell autoantibodies.

[0587] ENREF 47 ENREF 10 ENREF 48 ENREF 49 ENREF 49 The inventors show that the balance between costimulatory and coinhibitory signals that shape T cell exhaustion coincide with opposite clinical outcomes during autoreactive and anti-viral immunity. This at once allows prediction of outcome during infection and autoimmunity and creates the potential for targeted therapeutic exhaustion of an autoimmune response in those predicted to follow an aggressive disease course. That this association is apparent in multiple autoimmune and infection-associated immunopathologies emphasizes the importance of signals shaping T cell exhaustion in driving risk of relapse or recurrence (prognosis) rather than disease susceptibility (diagnosis) or immediate severity (disease activity), and suggests that targeted manipulation of these processes may lead to new treatment strategies that extend beyond the conditions discussed here.

TABLE-US-00001 TABLE 1 Upregulated/ downregulated in exhausted CD8.sup.+ T cell/ lack of GenBank SEQ CD4.sup.+ T cell Gene accession GenBank ID costimulation No symbol no. version no. NO. Description phenotype 1 KAT2B NM_003884 GI:156071487 1 K(lysine) acetyltransferase 2B gene downregulated 2 CASK NM_003688 GI:193788694 2 calcium/calmodulin-dependent downregulated serine protein kinase 3 gene 3 ABCD2 NM_005164 GI:168480147 3 ATP-binding cassette sub-family D downregulated member 2 gene 4 DLG1 NM_004087 GI:148539577 4 disks large homolog 1 gene downregulated 5 SS18 NM_005637 GI:815891164 5 synovial sarcoma translocation, downregulated chromosome 18 gene 6 RBL2 NM_005611 GI:172072596 6 Retinoblastoma-like protein 2 gene downregulated 7 RAB7L1 NM_003929 GI:208609960 7 RAS oncogene family-like 1 gene downregulated 8 MTHFD1 NM_005956 GI:222136638 8 methylenetetrahydrofolate downregulated dehydrogenase 1 gene 9 KERA NM_007035 GI:62865891 9 keratocan gene upregulated 10 BMI1 NM_005180 GI:323462179 10 B cell-specific Moloney murine downregulated leukemia virus integration site 1 gene 11 COG5 NM_006348 GI:240849530 11 conserved oligomeric Golgi complex downregulated subunit 5 gene 12 PDE4D NM_006203 GI:157277986 12 cAMP-specific 3',5'-cyclic downregulated phosphodiesterase 4D gene 13 VCY NM_004679 GI:49355825 13 variable charge, Y-linked gene upregulated

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Sequence CWU 1

1

1314824DNAHomo sapiens 1gcggaaaaga ggccgtgggg ggcctcccag cgctggcaga caccgtgagg ctggcagccg 60ccggcacgca cacctagtcc gcagtcccga ggaacatgtc cgcagccagg gcgcggagca 120gagtcccggg caggagaacc aagggagggc gtgtgctgtg gcggcggcgg cagcggcagc 180ggagccgcta gtcccctccc tcctggggga gcagctgccg ccgctgccgc cgccgccacc 240accatcagcg cgcggggccc ggccagagcg agccgggcga gcggcgcgct agggggaggg 300cgggggcggg gaggggggtg ggcgaagggg gcgggagggc gtggggggag ggtctcgctc 360tcccgactac cagagcccga gagggagacc ctggcggcgg cggcggcgcc tgacactcgg 420cgcctcctgc cgtgctccgg ggcggcatgt ccgaggctgg cggggccggg ccgggcggct 480gcggggcagg agccggggca ggggccgggc ccggggcgct gcccccgcag cctgcggcgc 540ttccgcccgc gcccccgcag ggctccccct gcgccgctgc cgccgggggc tcgggcgcct 600gcggtccggc gacggcagtg gctgcagcgg gcacggccga aggaccggga ggcggtggct 660cggcccgaat cgccgtgaag aaagcgcaac tacgctccgc tccgcgggcc aagaaactgg 720agaaactcgg agtgtactcc gcctgcaagg ccgaggagtc ttgtaaatgt aatggctgga 780aaaaccctaa cccctcaccc actcccccca gagccgacct gcagcaaata attgtcagtc 840taacagaatc ctgtcggagt tgtagccatg ccctagctgc tcatgtttcc cacctggaga 900atgtgtcaga ggaagaaatg aacagactcc tgggaatagt attggatgtg gaatatctct 960ttacctgtgt ccacaaggaa gaagatgcag ataccaaaca agtttatttc tatctattta 1020agctcttgag aaagtctatt ttacaaagag gaaaacctgt ggttgaaggc tctttggaaa 1080agaaaccccc atttgaaaaa cctagcattg aacagggtgt gaataacttt gtgcagtaca 1140aatttagtca cctgccagca aaagaaaggc aaacaatagt tgagttggca aaaatgttcc 1200taaaccgcat caactattgg catctggagg caccatctca acgaagactg cgatctccca 1260atgatgatat ttctggatac aaagagaact acacaaggtg gctgtgttac tgcaacgtgc 1320cacagttctg cgacagtcta cctcggtacg aaaccacaca ggtgtttggg agaacattgc 1380ttcgctcggt cttcactgtt atgaggcgac aactcctgga acaagcaaga caggaaaaag 1440ataaactgcc tcttgaaaaa cgaactctaa tcctcactca tttcccaaaa tttctgtcca 1500tgctagaaga agaagtatat agtcaaaact ctcccatctg ggatcaggat tttctctcag 1560cctcttccag aaccagccag ctaggcatcc aaacagttat caatccacct cctgtggctg 1620ggacaatttc atacaattca acctcatctt cccttgagca gccaaacgca gggagcagca 1680gtcctgcctg caaagcctct tctggacttg aggcaaaccc aggagaaaag aggaaaatga 1740ctgattctca tgttctggag gaggccaaga aaccccgagt tatgggggat attccgatgg 1800aattaatcaa cgaggttatg tctaccatca cggaccctgc agcaatgctt ggaccagaga 1860ccaattttct gtcagcacac tcggccaggg atgaggcggc aaggttggaa gagcgcaggg 1920gtgtaattga atttcacgtg gttggcaatt ccctcaacca gaaaccaaac aagaagatcc 1980tgatgtggct ggttggccta cagaacgttt tctcccacca gctgccccga atgccaaaag 2040aatacatcac acggctcgtc tttgacccga aacacaaaac ccttgcttta attaaagatg 2100gccgtgttat tggtggtatc tgtttccgta tgttcccatc tcaaggattc acagagattg 2160tcttctgtgc tgtaacctca aatgagcaag tcaagggcta tggaacacac ctgatgaatc 2220atttgaaaga atatcacata aagcatgaca tcctgaactt cctcacatat gcagatgaat 2280atgcaattgg atactttaag aaacagggtt tctccaaaga aattaaaata cctaaaacca 2340aatatgttgg ctatatcaag gattatgaag gagccacttt aatgggatgt gagctaaatc 2400cacggatccc gtacacagaa ttttctgtca tcattaaaaa gcagaaggag ataattaaaa 2460aactgattga aagaaaacag gcacaaattc gaaaagttta ccctggactt tcatgtttta 2520aagatggagt tcgacagatt cctatagaaa gcattcctgg aattagagag acaggctgga 2580aaccgagtgg aaaagagaaa agtaaagagc ccagagaccc tgaccagctt tacagcacgc 2640tcaagagcat cctccagcag gtgaagagcc atcaaagcgc ttggcccttc atggaacctg 2700tgaagagaac agaagctcca ggatattatg aagttataag gttccccatg gatctgaaaa 2760ccatgagtga acgcctcaag aataggtact acgtgtctaa gaaattattc atggcagact 2820tacagcgagt ctttaccaat tgcaaagagt acaacccccc tgagagtgaa tactacaaat 2880gtgccaatat cctggagaaa ttcttcttca gtaaaattaa ggaagctgga ttaattgaca 2940agtgattttt tttcccctct gcttcttaga aactcaccaa gcagtgtgcc taaagcaagg 3000tggtttagtt ttttacaaag aattggacat gatgtattga agagacttgt aaatgtaata 3060attagcactt ttgaaaaaac aaaaaacctc cttttagctt ttcagatatg tatttaaatt 3120gaagtcatag gacattttta ttttatggaa tagattttaa tctatttact actattaagg 3180taaattttct atggcatgtc cattagctat ttcatgatag atgattaggg gtttcctcaa 3240aacctgtgtg tgaggaaatt gcacacagta gcaaaatttg gggaaatcca taacattttc 3300agaccatgaa tgaatgtttc catttttttc taatggaatg tgagagttta cttttatttt 3360attctgaagg actttaagga agggatacat gattttaaaa aagcctgtaa gaggtgaaat 3420atgtgatgtt tgaagtctct ttatagactt tttatatata ttttttaaaa cactcatcta 3480gatgaggtgc tttgagcagt tctgaaaaat gcagttccag gaaagcaact gctttggttc 3540ctaaggaaga aattctaaat aatgcaaact tttaaaataa gcatctaggt ttttgataat 3600tctgtctact tacaacaaac ttgttagtac ataaccacta ttttaataat tattttctct 3660acacaaatgt gtaatatcat atttgacttt gcttatgcag gccataagtt ccaaaagata 3720atttccctgc ccacaaaggc ataaacttga aaacacatga gattgaatca acatgcttta 3780ataggaaaag atgtatggtc tatatatgta tcaatctggt gaatcctcgt tctaataaag 3840gttctttttc ttttctatga tacacacagc cacgctgata atatgcaaat gaacattttc 3900ctttatgtct ctccagataa tgtttattgt ctgaggtaaa ttaaattccc accagggttt 3960gctgtcagta ttttaacacc cacattagta tatgcgtcca gggtcataac cccctaaaat 4020ccatcatgca accttattaa tctgtcttgg gattccagtt tagtgcttgg atttatttcc 4080tgattacact acatagaaaa gtgagacatc tgccattccc aactctggga aaaccaacta 4140atatacaacc atataaatga aggccatctt gatggtctca acactaattt ttatgatgca 4200aatttataca ctgatttttg taaaggacaa agttttaaaa gcgtatttaa cttgatgttt 4260tctatcagca taaataaaat ggtcatgaat agtcattaaa aacagttgcc agtgataatc 4320tgcatgaagg aaaaagaacc ctgcaaatgg ctattgagtt ggaagtattg tttttgatat 4380gtaagagata ttcagaatgc tcacactgaa aatgcctcaa ctttttaaag tgtaagaaac 4440caccatgagt ggtgtctaga tttctaatga agaatcatga tacagtttgg attaagtatc 4500ttggactggt tttaaacagt gctttgtacc ggatctgctg aagcatctgt ccagctggta 4560tcctgtgaaa gtttgttatt ttctgagtag acattcttat agagtattgt ctttaaaatc 4620agattgtctc ttctatattg aaagcatttt tatgttttct aatttaaaaa ttaatatttt 4680cttatagata ttgtgcaata aagctgaagt agaatgtgtg gtttttgcaa atgctttaac 4740agctgataaa aattttacat ttgtaaaatt aatatattgt actggtacaa aatagtttta 4800aattatattt taaaaagctt ccaa 482428298DNAHomo sapiens 2ccgttttcga agccctccac gctgcggccg ctatcccctc cggaccatgg ccgacgacga 60cgtgctgttc gaggatgtgt acgagctgtg cgaggtgatc ggaaagggtc ccttcagtgt 120tgtacgacga tgtatcaaca gagaaactgg gcaacaattt gctgtaaaaa ttgttgatgt 180agccaagttc acatcaagtc cagggttaag tacagaagat ctaaagcggg aagccagtat 240ctgtcatatg ctgaaacatc cacacattgt agagttattg gagacatata gctcagatgg 300aatgctttac atggttttcg aatttatgga tggagcagat ctgtgttttg aaatcgtaaa 360gcgagctgac gctggttttg tgtacagtga agctgtagcc agccattata tgagacagat 420actggaagct ctacgctact gccatgataa taacataatt cacagggatg tgaagcccca 480ctgtgttctc cttgcctcaa aagaaaactc ggcacctgtt aaacttggag gctttggggt 540agctattcaa ttaggggagt ctggacttgt agctggagga cgtgttggaa cacctcattt 600tatggcacca gaagtggtca aaagagagcc ttacggaaag cctgtagacg tctgggggtg 660cggtgtgatc ctttttatcc tgctcagtgg ttgtttgcct ttttacggaa ccaaggaaag 720attgtttgaa ggcattatta aaggaaaata taagatgaat ccaaggcagt ggagccatat 780ctctgaaagt gccaaagacc tagtacgtcg catgctgatg ctggatccag ctgaaaggat 840cactgtttat gaagcactga atcacccatg gcttaaggag cgggatcgtt acgcctacaa 900gattcatctt ccagaaacag tagagcagct gaggaaattc aatgcaagga ggaaactaaa 960gggtgcagta ctagccgctg tgtcaagtca caaattcaac tcattctatg gggatccccc 1020tgaagagtta ccagatttct ccgaagaccc tacctcctca ggacttctag cagcagaaag 1080agcagtctca caggtgctgg acagcctgga agagattcat gcgcttacag actgcagtga 1140aaaggaccta gattttctac acagtgtttt ccaggatcag catcttcaca cactactaga 1200tctgtatgac aaaattaaca caaagtcttc accacaaatc aggaatcctc caagcgatgc 1260agtacagaga gccaaagagg tattggaaga aatttcatgt taccctgaga ataacgacgc 1320aaaggaacta aagcgtattt taacacaacc tcatttcatg gccttacttc agactcacga 1380cgtagtggca catgaagttt acagtgatga agcattgagg gtcacacctc ctcccacctc 1440tccctattta aacggcgatt ctccagaaag tgctaacgga gacatggata tggagaatgt 1500gaccagagtt cggctggtac agtttcaaaa gaacacagat gaaccaatgg gaatcacttt 1560aaaaatgaat gaactaaatc attgtattgt tgcaagaatt atgcatgggg gcatgattca 1620caggcaaggt acacttcatg ttggtgatga aattcgagaa atcaatggca tcagtgtggc 1680taaccaaaca gtggaacaac tgcaaaaaat gcttagggaa atgcggggga gtattacctt 1740caagattgtg ccaagttacc gcactcagtc ttcgtcctgt gagagagatt ccccttccac 1800ttccagacag tccccagcta atggtcatag cagcactaac aattctgttt cggacttgcc 1860atcaactacc caaccaaaag gacgacagat ctatgtaaga gcacaatttg aatatgatcc 1920agccaaggat gacctcatcc cctgtaaaga agctggcatt cgattcagag ttggtgacat 1980catccagatt attagtaagg atgatcataa ttggtggcag ggtaaactgg aaaactccaa 2040aaatggaact gcaggtctca ttccttctcc tgaacttcag gaatggcgag tagcttgcat 2100tgccatggag aagaccaaac aggagcagca ggccagctgt acttggtttg gcaagaaaaa 2160gaagcagtac aaagataaat atttggcaaa gcacaatgca gatcttgtca catatgaaga 2220agtagtaaaa ctgccagcat tcaagaggaa aacactagtc ttattaggcg cacatggtgt 2280tgggagaaga cacataaaaa acactctcat cacaaagcac ccagaccggt ttgcgtaccc 2340tattccacat acaaccagac ctccaaagaa agacgaagaa aatggaaaga attattactt 2400tgtatctcat gaccaaatga tgcaagacat ctctaataac gagtacttgg agtacggcag 2460ccacgaggat gcgatgtatg ggacaaaact ggagaccatc cggaagatcc acgagcaggg 2520gctgattgca atactggacg tggagcctca ggcactgaag gtcctgagaa ctgcagagtt 2580tgctcctttt gttgttttca ttgctgcacc aactattact ccaggtttaa atgaggatga 2640atctcttcag cgtctgcaga aggagtctga catcttacag agaacatatg cacactactt 2700cgatctcaca attatcaaca atgaaattga tgagacaatc agacatctgg aggaagctgt 2760tgagctcgtg tgcacagccc cacagtgggt ccctgtctcc tgggtctatt aggcctctcc 2820ccagatatct gagcataact gggagcacct catttgtgga aaagcctctt tgttatcggc 2880cttgtgtcag caggtcatgg tccctagaga ctacctagtt gtagtgtgac ctacatttat 2940aattattgtc atgtccgaat agataggagg agaaaaacaa ttacacacta atttaaagag 3000acagtatctt ttttaatcag ttctcctaaa ctttaataaa atgtatcttt aaatgtatgt 3060attattcaat cctttggaat gttatatttt tggaaatcat agctttttat ttccaaggcc 3120cctaaaaact gcacaaaata gatgctgctt tctataatct attttaataa taataaacaa 3180tgattctgtt accttgactg ggggtggaac actacattct ttttagagtc tgattttatg 3240gattggaata ttgggatatc tttctttcct ttatttattt gaaataatta gtgtagtgat 3300tacaaaacag tcataaattt ttaaaggcct tttttctctc tttttttttt tttagaatag 3360tatttttttt taagtccttt atgtaacatc cagataatgt gatactgtct ctttgaagca 3420ccctgtaaac cttttagaga tttgaagttg ggtcttgact cttaatgcat gtggacagtc 3480gcgagcgttt atgctgtcgg tgtgtctgtg ttggacaaaa caatctgtaa tctacagcaa 3540agtacattct acattccgtt catggggcac acccagggga ataagaataa aatgctatta 3600tgactaagtt gtaaacctat gcacatccct tgcattttgg gcaactttat aaaaaaaaag 3660aaactgattt ttattaataa taatcatgta gtgaaatgtg tttgtaattt tgtctcaatt 3720taatttgttg taaggtgggg tggggggaat tgctggtttc accatttcag atctgtgttg 3780tctaagagta ttaacgtttt aattaagcaa agaaatgatt tttaatctgt atgtaattgt 3840tttaaagcac ccattttaag agaaaatact gtgcaatgaa gaaaccagtt taggcatttg 3900ctataaactg aaatattcca aaagaatcat ctataacagc cctgtaaatt cctttaaaat 3960gataactaac aggacagttt gaccaatttt ttttaaatat acttcctttt atgtgttcaa 4020taattaaatg cctttgggtc cttcatttca ttatagattt gttcaggctt ccaagctgat 4080aatctttaca attgtataat ttgttagatg ctcattgaac ctttgaaggc ccaggagtga 4140gtatcagttg gcagggtgac aaagtagcct gccagagcac agctggacca cgtctgactc 4200gcacagagcc atgcgcccaa gggccacggg tgtactggag gccacctgtg gtctctcctt 4260cctcttgctg tatcccttgg cacaggggaa tcatctgtcc ttgttgcttt agagacatta 4320accatctcat aactcttcca tgaagtcaca ttcttccaat acaggagatt cgggctgggg 4380ttctcagact ctttgccaga ggtcagtaga atgtttttca ttagcatgtg agggtgtgaa 4440gtgcttatat taacctgtga tccttgaaaa cataccatca ttttttgctt cttgtaggtt 4500agatggcctt gtcactttgt gccttggcag gatgtgcagg gtgtgttctg agctgaacag 4560ctcctcttaa aggaccaaac agagaaggca ttagtatact tcttttacat tgtcaacacc 4620atacccgcct ccgcccccca ccgcctatta ttaaatggtg gcgatttttt tttttctgat 4680gttgttcttt gccagtgacc agatgagtct gcaacttact aacaaggtat tgagtgaact 4740acttctgtat gggccccaca gtggggtgac caagccacca aaccagagat aagctcaaca 4800gtggtctcac actagataga gagagaaacc ttcaaagagt tgggtagggc tgtgttagaa 4860ctgattcgaa tctgatagat gccaaggcca gacagtcgtt cctggtatgg tactgaccac 4920aatttcgggc tcttagtgtg aaggtgcgca ctctacctct tttctggtga agcacaaaga 4980caactacaac taacacatgg gaaacagaaa cttccctccc tctagtggaa acccccacgc 5040ccccacttgc cctttgagcc cacatctcca gagatgctga tgatgcctgt cttaagccat 5100ctgccatatt tataaaggtg gattaagcag aggaggagaa aagcaatgcc aacttaaatg 5160tctgtggccc cacaattcac aagcactgta gcactcatcc tcagtggctt tatacgtcct 5220ctgagaagca cacaggcagg catcattctt gccatcattc cgatggtgaa atccctgcat 5280gcagaactca ttgacttctc aaagatgtta cctgttccat tccactaata catgtcttct 5340ctaaagcagt gtctttatga cctagctgca tatacttaca tttctgaatt cagagtaatt 5400tcagtacatt gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc 5460tactgctaca ttacaattgt ccactaagca atcagagaaa attgctaaaa gcttctttac 5520tgcttccatt ccatcagcag aacctttttt tttctttctt tcttttaaag accagaatga 5580atgtttagag tactaaatct tattagtggt caattgaagt attggagagc cacattttga 5640aggttctctc ccccacccaa ctccattccc cacagcaaga aagggagtgt ttttatatgt 5700tgaattcttt gttaaaaaga tgaaatgtcc tgattttcca gtcacaagac agtaattact 5760ttgcacatac agcatatccc attttaatgc taaaaaggga aatgtcactc aatttaattc 5820atctggaagt ttcccagtgt caagataaca ttgtagcctt tttaaatgca attaaatgta 5880tctcttgtca ggtgagatga tttaaaatct ttgctcagag aggaaaacaa atggttgacc 5940tacttcttgc tatttgcatt cagaaggcat cgtcccagcc catcctattg gtggcagaat 6000atctaaagat gtcgcaaagt cccccactgc agtagaaatg caggaggtgt tcctgttccc 6060cgtccaattc cttcttaggc tgctagagac agccagtggg ccaagccttc ccctgtgctc 6120caggcaggcc tgggctgcag ctactgttac ctttttacag cctttgatct gatcgctgca 6180gagttctttt gtttttaaat cacttgtatt tgtctcttca ttaaggcttc aagtttattt 6240cttgaaaaag tttagtcaat tgaaccaccc tccaggaaga ttcccagcgt ggaaactgcc 6300cctgaaaaac aaggcagccc aaagccagct ctcttttgtc ccccactgat gtcatgtcct 6360tttttttttt catttcaggc cagtttctta acttggggca aagagaatgt gttgctaaag 6420ctaccaagaa aactgcttga ttaacaaatt cttaatagaa atgcctccca cactgtctct 6480ttgaaaagag aaggcacctt ggaatcggca ttccaaaacc aagctccttg tcatcctcat 6540ccctcctcct tcttgcttcc tattatcaaa ctcgtgtgtg tttcttgttt tctcagaact 6600gaacacagcc tcctaattcc atcctcttga ctagggctta caatactgag agcgattaca 6660ggctgtaata agttaaaggt ccctgagcgt ggctttcttg ttctgcgcct ctaattaatt 6720cttctattaa aagatgcttt ccttctcact gcagcttaca gaaaggctac aagctttaat 6780cacagatcat ttcatttgcc agagcctttc cttttctaac tcctttagaa ataagatttc 6840cctctctgtt tggaatctct ggatacagga ctctcctcca agctcatggc ttgattggct 6900ttgcctgtgc acacacacat cagtttgcct taaacttgga gctatgggga gtcccagatt 6960ttccagctta gtgggtgaag tttagctgtc acctacatcc aggaagtggg ggaaaaggga 7020aaaaaagagg atattcacca ccatgttccc atccggtctt tcccctgcct tgctttgtgc 7080agcaggtggg cagacagagc ccacagaaac agaagtagaa agagggccgc accatctctg 7140gggccagcac tcctaagtct tagctctttg tgggaataga aaatcctgag ctcccaccac 7200ctctcgtctg accctccatc aactccctcg aacctgtgca aatggactga gcaaaagaaa 7260atggaaagag atgtttgtca ccacacagga gacctccttt ctggccccaa gcacaactcc 7320atctctgcgt atgctcagaa actcagaatt tagctgctac ttatgtgtta gctccattct 7380ctctggtgtg tgactgagag aacacgccag tgttcttact gacagaggct taggggtgac 7440cctctctgga cccagaggaa gtacaacctc tgtagcgaga attgtccttg ggaacagaaa 7500caggcattcc tccacagtga gtggctcccc ctattttttt tttatttgga agagaccaag 7560aattggggga attgatttcc agtcttagct gtttcccgga atgtcatctg tgcaggcagg 7620taggcggctg ccgggtgcag caggcagcgt gactgatgtg aaggccgccc aatcctcacg 7680tgctaagacc cgagtatcgt gtttaattgc agtgtaggca cgtcgccatt caaactcagt 7740tctggggtgg ttttgcataa agttttgcca acgtgttctt ttttctgtat gtattattgc 7800ctttttataa aaggtgttga agtattgtct cagtgataaa aagagagaga tgttaatggt 7860tgttgtatat ttcaccgtat ccaattgtaa gtatttgcag ggtacagcag agccttagct 7920tgcaagagcg tttgtgcagg aggtgtccct caacacccag gagctgaagg gattggaaag 7980gtttggattc tttgtaaatg tcctgctttt ctttctctct gtgtgtatct atttacatgc 8040cttagcacac gccctcccat cctgatccct ttgccctgtc gccggaacaa ccagaatgct 8100ggtgcgctgc cggcacagta caagttgatg aaaccctaat cagttatctt gtgtgacagg 8160ggaagaagag aaactccata gtattccttg tagaatatac atacctgtag gatgctgtgt 8220aatgggaaac catagaattg ggcttttgtc atttcaaagt tggagaaatg tatgaataaa 8280atgtataaaa catgaaaa 829835341DNAHomo sapiens 3agctagagcc ggttttgttc gccagcagat ggcctgattc gacctctcca aaaatagaca 60ttttaactct ctgaactcct gtttaaggaa ggatgtaatt cgctttgctc tctcctcatt 120ttcaaggttc aaagggaagc tgcgaggatt ccaaggtccc accgccctca cagccaatga 180ggggcctggg agggaggagc ttggtgcagc ttgagcttct gagagaatca ttcccggtag 240atgcagcgga gtctgagctc tgctgcatct gtcacagcag aacaaaatta aaaacacaac 300agtggaagag aaacgctgca gactatggga cgctgtagga ctttctaaaa catttgctgg 360ggatttctgt gaagcatgat cttttaaaac gaattctttt ggaagccggt ttgggtaact 420gggaaaatga cacatatgct aaatgcagca gctgatcgag tgaaatggac cagatcgagt 480gctgctaaga gggctgcctg cctggtggct gcggcatatg ctctgaaaac cctctatccc 540atcattggca agcgtttaaa gcaatctggc cacgggaaga aaaaagcagc agcttaccct 600gctgcagaga acacagaaat actgcattgc accgagacca tttgtgaaaa accttcgcct 660ggagtgaatg cagatttctt caaacagcta ctagaacttc ggaaaatttt gtttccaaaa 720cttgtgacca ctgaaacagg gtggctctgc ctgcactcag tggctctaat ctcaagaacc 780tttctttcta tctatgtggc tggtctggat ggaaaaatcg tgaaaagcat tgtggaaaag 840aagcctcgga ctttcatcat caaattaatc aagtggctta tgattgccat ccctgctacc 900ttcgtcaaca gtgcaataag gtacctggaa tgcaaattgg ctttggcctt cagaactcgc 960ctagtagacc acgcctatga aacctatttt acaaatcaga cttattataa agtgatcaat 1020atggatggga ggctggcaaa ccctgaccaa tctcttacgg aggatattat gatgttctcc 1080caatctgtgg ctcacttgta ttccaatctg accaaaccta ttttagatgt aatgctgacc 1140tcctatacac tcattcaaac tgctacatcc agaggagcaa gcccaattgg gcccacccta 1200ctagcaggac ttgtggtgta tgccactgct aaagtgttaa aagcctgttc tcccaaattt 1260ggcaaactgg tggcagagga agcacataga aaaggctatt tgcggtatgt gcactcgaga 1320attatagcca atgtagaaga aattgccttt tacagaggac ataaggtaga aatgaaacaa 1380cttcagaaaa gttacaaagc tttagcagat cagatgaacc tcattttatc caaacgtttg 1440tggtacatca tgatagaaca gttcctgatg aagtatgttt ggagcagcag tggactaatt 1500atggtggcta tacctattat cactgcaact ggctttgcag atggtgagga tggccaaaag 1560caagttatgg ttagtgaacg gacagaagcc tttaccactg ctcgaaattt actggcctct 1620ggagctgatg ctattgaaag gattatgtct tcatacaaag aggtcactga attagcaggc 1680tacactgctc gagtgtacaa tatgttttgg gtctttgatg aagtaaaaag aggcatttat 1740aagagaactg ctgtcattca agaatctgaa agccatagca agaatggagc taaggtagaa

1800ttacctctca gtgacacatt ggcaattaaa ggaaaagtta ttgatgtgga tcacggaatt 1860atttgtgaaa atgttcccat aattacacca gcaggagaag tggtggcttc caggctaaac 1920ttcaaagtag aagaaggaat gcatcttttg ataactggtc ccaatggttg tgggaaaagt 1980tctctcttca gaattctaag tgggctctgg cctgtgtatg aaggagtcct ctataaacca 2040cctcctcaac atatgtttta tattccacaa aggccatata tgtctcttgg aagtcttcgg 2100gatcaagtca tttaccctga ttcagtggat gatatgcatg ataaaggtta tacagaccaa 2160gatctggaac gtatcctaca caatgtccat ctctatcaca tagttcaaag agaaggagga 2220tgggatgctg ttatggactg gaaagatgtc ctgtcaggag gggaaaagca aagaatgggc 2280atggctcgta tgttttatca taaaccaaaa tatgccttgc tggatgaatg taccagtgct 2340gtcagcattg atgtcgaagg aaagatattt caggctgcaa aaggggctgg aatttcctta 2400ctgtctataa cacacagacc ttctctttgg aaataccaca cacatttatt acagtttgat 2460ggtgaaggag gttggcgctt tgaacaattg gatactgcta tccgtttgac attgagtgaa 2520gaaaaacaaa agctagaatc tcagctagct ggaattccca aaatgcagca gagactcaat 2580gaactatgta aaattttggg agaagactca gtgctgaaaa caattaaaaa tgaagatgag 2640acatcttaat ttgttttgac atattttaaa agttaattat tagataaagg ctcaaagaca 2700ttctgttata ctgcatgaag tatgttaagc taagcacaga gaaaaaaagg cagcaagaca 2760tgttttataa gattttagca ttaaggaagt atatgatctg acttttcaga agaaaataaa 2820caaatgcatt atgtaaggtc agtcattatg acttatacta attcctagtg aaggcctaat 2880gcacttgtaa aacaggattt tctaggtgaa ttcatgatga ataccagatt tactatgtat 2940atgtggtgtg tctgaagttc ttaacaaaca tgggcaatat tctggaaatg aaacaagtta 3000aactgagcag catttgggtt gataccaagt gcataagatt caaactttga gtgacattta 3060gtccatttat ggttgatatt aggtttaata gctagaattc aaattgatta ttgctagtgg 3120ccaactaaac ctgtacaaaa tagctgacag ttttataaat aatttcaata taaaaattgt 3180tttaatggca tttgttgaaa gaaaaaagca tggctaaaat gtataaaatg ccatattttt 3240aaattttgga ctttaagcat cttaatgagg gcatataaca aattaatttt agtacaaatc 3300ttaaatattt ttaataaatc ctttcatttt aaaaagagaa ttgccaatac agaaaaggag 3360tatccaaaca atgtctcaac ctgataattt ccttagcaga attacctatt gcaacttctg 3420ttcagaaata cacagcttgt ttttttgccc aaggatgagt ctacatttta agaactgcaa 3480tggtataaag gaacttaagg attctgagaa tcatagtaat aacatacatt ggaatagtac 3540tttataattt acaatcccca tttacatcat ttcaccttaa tgttgatgac aatgttttga 3600aacaaatact atttttccta ctttgctttt gagaaaattg acactcagac ttgccctaat 3660catgcacttt acttaaggaa agatcgagaa atcaaatgaa gttctcctga ctctctggtt 3720tagtgctctt ttgttattat cctttaaatc aaactgggct ataatagcaa taaaagttag 3780acgaagtgta gaaaataaaa taaatttcat aatgttagtc ttattgttat ttggttattg 3840tttacaagaa atgaaaatta agtacaaagt gcaaagatca ttgttctgcg gcttaaaatg 3900aaatgagaaa gttagtaaat cattcagcaa ctatgcagtc ttactcaata ttaatgtacc 3960tctaaggcat tagcaatgag aagggcaaat aattatggtt ttggtaaagt taatatttat 4020tgaacataat gagaaataat ctatatggac tagtcatatg aaatagattt tattctattt 4080gtgtgcactg gagctggaaa gccaagactg aaactttatc tcttgctgcc tgtgatacca 4140cattgacata ccagaagaat attggaatga tcagttgtta gtggcctagg attttatttg 4200cctgttgaga cacagccata atagatgtta agtctgtgat tcttagactt ttcaggtgat 4260agagtacctg gaagtcattc ataatgatcg ttatagaaca tcataacatt tctacatttt 4320caattctgcc atgatagcta gtgtattttt aattttcaat aaatgtaacc aacttacatg 4380aaggaatgca atataaaatt ataatcagta catttgtcca acgttttcat tagtattatc 4440acctacttat tcatcagtta ctaatatttc ctgttagaaa agtgaggcag gaattaaaga 4500ttttttttta agaagcatgg aaccaaaact taaacttgct aaaaattatt cattaatctt 4560ttctacataa gtgattatcc agtttatact gctacaaggg caaaagtctg aggcaagtgt 4620tttaagttaa cttttaaagg tacaagaaga aaatgaaaaa tcctcatgtg aaagatgtgt 4680ataattttca tgccttaatt ttcataatat aaaaataaaa cataatttta aaacaacctg 4740ataattttgt tttgaaacat tgaaaagaat gccaaaacaa atattagatt tgtaattagt 4800cagtatttaa tatattttac ccatgagcta aagcaaaaaa gactcattat ttatgatgca 4860caggattcaa agatgcctaa aattctgtat taaaaactat gtacactgta atttaaatgt 4920taaagttcta atatgcacat gttttccatg agctttttgt gcctatttgt tttctgaatt 4980tatttttcag gaccaacatc cttaacttgg aagggaaaac atctctgatt tgaacttgta 5040tttatgtacc attcaattgt ttccaaatgg tccaatgggt ataccatatt ttactactct 5100tatattttac ggaaaacatg aaaaagactg agaaactagc catttttgaa tacagcaagg 5160gatagatgag gaaaggaaaa aagaaagaat atttcaagtt tcaaactact tttaccatgt 5220tatatctatt tgcccaaacg tttgacatat ttttggtcaa acaaaaagct ataagtttat 5280ggagcttgag tttaaaatgt gcattcttta ggttaactct taaacttgaa aaataagttg 5340g 534145034DNAHomo sapiens 4gttggaaacg gcactgctga gtgaggttga ggggtgtctc ggtatgtgcg ccttggatct 60ggtgtaggcg aggtcacgcc tctcttcaga cagcccgagc cttcccggcc tggcgcgttt 120agttcggaac tgcgggacgc gccggtgggc tagggcaagg tgtgtgccct cttcctgatt 180ctggagaaaa atgccggtcc ggaagcaaga tacccagaga gcattgcacc ttttggagga 240atatcgttca aaactaagcc aaactgaaga cagacagctc agaagttcca tagaacgggt 300tattaacata tttcagagca acctctttca ggctttaata gatattcaag aattttatga 360agtgacctta ctggataatc caaaatgtat agatcgttca aagccgtctg aaccaattca 420acctgtgaat acttgggaga tttccagcct tccaagctct actgtgactt cagagacact 480gccaagcagc cttagcccta gtgtagagaa atacaggtat caggatgaag atacacctcc 540tcaagagcat atttccccac aaatcacaaa tgaagtgata ggtccagaat tggttcatgt 600ctcagagaag aacttatcag agattgagaa tgtccatgga tttgtttctc attctcatat 660ttcaccaata aagccaacag aagctgttct tccctctcct cccactgtcc ctgtgatccc 720tgtcctgcca gtccctgctg agaatactgt catcctaccc accataccac aggcaaatcc 780tcccccagta ctggtcaaca cagatagctt ggaaacacca acttacgtta atggcacaga 840tgcagattat gaatatgaag aaatcacact tgaaagggga aattcagggc ttggtttcag 900cattgcagga ggtacggaca acccacacat tggagatgac tcaagtattt tcattaccaa 960aattatcaca gggggagcag ccgcccaaga tggaagattg cgggtcaatg actgtatatt 1020acgagtaaat gaagtagatg ttcgtgatgt aacacatagc aaagcagttg aagcgttgaa 1080agaagcaggg tctattgtac gcttgtatgt aaaaagaagg aaaccagtgt cagaaaaaat 1140aatggaaata aagctcatta aaggtcctaa aggtcttggg tttagcattg ctggaggtgt 1200tggaaatcag catattcctg gggataatag catctatgta accaaaataa ttgaaggagg 1260tgcagcacat aaggatggca aacttcagat tggagataaa cttttagcag tgaataacgt 1320atgtttagaa gaagttactc atgaagaagc agtaactgcc ttaaagaaca catctgattt 1380tgtttatttg aaagtggcaa aacccacaag tatgtatatg aatgatggct atgcaccacc 1440tgatatcacc aactcttctt ctcagcctgt tgataaccat gttagcccat cttccttctt 1500gggccagaca ccagcatctc cagccagata ctccccagtt tctaaagcag tacttggaga 1560tgatgaaatt acaagggaac ctagaaaagt tgttcttcat cgtggctcaa cgggccttgg 1620tttcaacatt gtaggaggag aagatggaga aggaatattt atttccttta tcttagccgg 1680aggacctgct gatctaagtg gagagctcag aaaaggagat cgtattatat cggtaaacag 1740tgttgacctc agagctgcta gtcatgagca ggcagcagct gcattgaaaa atgctggcca 1800ggctgtcaca attgttgcac aatatcgacc tgaagaatac agtcgttttg aagctaaaat 1860acatgattta cgggagcaga tgatgaatag tagtattagt tcagggtcag gttctcttcg 1920aactagccag aagcgatccc tctatgtcag agcccttttt gattatgaca agactaaaga 1980cagtgggctt cccagtcagg gactgaactt caaatttgga gatatcctcc atgttattaa 2040tgcttctgat gatgaatggt ggcaagccag gcaggttaca ccagatggtg agagcgatga 2100ggtcggagtg attcccagta aacgcagagt tgagaagaaa gaacgagccc gattaaaaac 2160agtgaaattc aattctaaaa cgagagataa agggcagtca ttcaatgaca agcgtaaaaa 2220gaacctcttt tcccgaaaat tccccttcta caagaacaag gaccagagtg agcaggaaac 2280aagtgatgct gaccagcatg taacttctaa tgccagcgat agtgaaagta gttaccgtgg 2340tcaagaagaa tacgtcttat cttatgaacc agtgaatcaa caagaagtta attatactcg 2400accagtgatc atattgggac ctatgaaaga caggataaat gatgacttga tctcagaatt 2460tcctgacaaa tttggatcct gtgttcctca tacaactaga ccaaaacgag attatgaggt 2520agatggaaga gattatcatt ttgtgacttc aagagagcag atggaaaaag atatccagga 2580acataaattc attgaagctg gccagtataa caatcatcta tatggaacaa gtgttcagtc 2640tgtacgagaa gtagcagaaa agggcaaaca ctgtatcctt gatgtgtctg gaaatgccat 2700aaagagatta cagattgcac agctttaccc tatctccatt tttattaaac ccaaatccat 2760ggaaaatatc atggaaatga ataagcgtct aacagaagaa caagccagaa aaacatttga 2820gagagccatg aaactggaac aggagtttac tgaacatttc acagctattg tacaggggga 2880tacgctggaa gacatttaca accaagtgaa acagatcata gaagaacaat ctggttctta 2940catctgggtt ccggcaaaag aaaagctatg aaaactcatg tttctctgtt tctcttttcc 3000acaattccat tttctttggc atctctttgc cctttcctct ggagtctttc ttgagtactg 3060atttcatgtt gaattgtatc ccacacatca tggtctgcag cttctttttc acatgtagtg 3120tctccttcaa gttacatcgt gtgtattatt taatgtcact attggttagt ggccattttt 3180cagaactgaa gatggaatgg cctgaccagc tattaagaac gtggggagac gcagaaattg 3240tggtaaaatt ccttaatgtt taagggaaag taactttaag agatttttgg aaaagcttta 3300tatacattct tttcaaattt cagtacaaat gaaaaagtgg ttttaatcag tgatttagta 3360gactttgagc aactgtgcac gcttcagttt aatagcatgg tttggccagt gtattactct 3420caagtccttt tctcaatcaa cttctatcat caaagcaatt gtttcattat agataaataa 3480ggacattttt taatttaaaa attcatgtct gagttgactt tcataaggga tttcattttt 3540tcctcaacat tcttaaagcc ttttagtatt tgacggttct tttttcccag gacatttgct 3600aggaataaca acgtttcaat gtttttaatc tacttgagca acactatcgt gtcttacaaa 3660agttgttcat atgtaaatga tcatcacatt tcgtgaattg aggccatgtt caggtgctaa 3720ggaagttcgc cttttacaca gaagattgag aaaatttcct agatataaat acagataaat 3780cagacgttac agtggtgacg tagtaaccat catggcaatg gaaaggagtc caattcatag 3840cctaaaactt caaatgtatt cttaggagtc agattttact gaatatttta cccacaatag 3900ctgcctattt tgttataata aaatatatat aaatatatat ataaaacttt ctttaaactg 3960taactatggg aattattttc tttacatagt tgcgcacaca cacaaacata tatatatatt 4020taaaatatat tttgtttctt ttgccaccta ctcctaactt tttgtttggt ttttaaatta 4080aatattaatt gaatagactt atcttcctta atcatgtgaa ctgaaaatgg gggcatggtg 4140gtcatgagga ggaaacattt agggaaatta gattataagt aaaagtgtgg gcatattctc 4200ctcttttcta caaaggtttt caaatggttc ctgaggtttt ttgttgttgt ccgtgttgtt 4260actgttgttc ttgtcatcag gtttgatttt ggtccttgcc ctttccttct agttctcctt 4320ttattaatag gaaggcaggc aaaagcccca tttatgtgtg tgttttcccc tcagacagct 4380ttcatccact gctctgcact agaattgcac aaatcttcat ggtgagcaat tttaagaaat 4440gttagtgaaa ggtagaaatt atttcacaaa tcagtttctc tggtccttca tattaataat 4500aatatttggc ttcccattgc tctttggagt tgtttattaa atatgtgttt ttgacaacct 4560cctcattagt ttcttaaatg agtactggtt tgtaaagaat tatcaacatt atccattcca 4620tttatgaaga agaggagaac agctaataaa ctgtattgta aaatccatat gttaagtgtg 4680tcttgaattt tgaaagaaaa aatatatttt gcaagctaac attttcttga aacaatttga 4740ggcatcatgt aacttataac cgaatccaag agccgttagg cagcagagtg tgttaccaca 4800ttgaaataca cagtgctgct gttagactaa atgtcgtagg ttgttaacca catagaaaca 4860cactagtatg aagaaaactg ttgtaaaatc tcaagagctt cagaaactgc cttacaagac 4920cgcagcataa gctattttga agtatttacc aaatagtcac atgttgtaaa atatcaagtg 4980gttataaaag gatgccattt atatattaaa atttacataa cattgttttc tgga 503453347DNAHomo sapiens 5gagaggccgg cgtctctccc ccagtttgcc gttcacccgg agcgctcggg acttgccgat 60agtggtgacg gcggcaacat gtctgtggct ttcgcggccc cgaggcagcg aggcaagggg 120gagatcactc ccgctgcgat tcagaagatg ttggatgaca ataaccatct tattcagtgt 180ataatggact ctcagaataa aggaaagacc tcagagtgtt ctcagtatca gcagatgttg 240cacacaaact tggtatacct tgctacaata gcagattcta atcaaaatat gcagtctctt 300ttaccagcac cacccacaca gaatatgcct atgggtcctg gagggatgaa tcagagcggc 360cctcccccac ctccacgctc tcacaacatg ccttcagatg gaatggtagg tgggggtcct 420cctgcaccgc acatgcagaa ccagatgaac ggccagatgc ctgggcctaa ccatatgcct 480atgcagggac ctggacccaa tcaactcaat atgacaaaca gttccatgaa tatgccttca 540agtagccatg gatccatggg aggttacaac cattctgtgc catcatcaca gagcatgcca 600gtacagaatc agatgacaat gagtcaggga caaccaatgg gaaactatgg tcccagacca 660aatatgagta tgcagccaaa ccaaggtcca atgatgcatc agcagcctcc ttctcagcaa 720tacaatatgc cacagggagg cggacagcat taccaaggac agcagccacc tatgggaatg 780atgggtcaag ttaaccaagg caatcatatg atgggtcaga gacagattcc tccctataga 840cctcctcaac agggcccacc acagcagtac tcaggccagg aagactatta cggggaccaa 900tacagtcatg gtggacaagg tcctccagaa ggcatgaacc agcaatatta ccctgatgga 960aattcacagt atggccaaca gcaagatgca taccagggac cacctccaca acagggatat 1020ccaccccagc agcagcagta cccagggcag caaggttacc caggacagca gcagggctac 1080ggtccttcac agggtggtcc aggtcctcag tatcctaact acccacaggg acaaggtcag 1140cagtatggag gatatagacc aacacagcct ggaccaccac agccacccca gcagaggcct 1200tatggatatg accagggaca gtatggaaat taccagcagt gaaaaagtac ttacattcca 1260gtagccagta tctattagca gccatattgt cacctcagca ctgtggacac ctccctgtga 1320agagatcctt ccattccatc tagtttttgg aaaaaccttg tggataagtg gctgtttcat 1380cagtaagcag cctttgtggt ttagttataa aaggctttag tagctcaaaa atactcttga 1440tttcacattt ctactctaga tggcaacatt ggacagaaaa tgcaatgaca taaccaattt 1500gtaatgattt tggaactgtg tttcaaatgg actgttacag actgaaaggt gtgaacagct 1560ttgtatgttt atgaagggta agggaattta atacttttcc acagattttt ttgtaagggg 1620aagagggaaa tgtacacttt ttacagcagc aatattttgt atattatgtt tatttcatgt 1680ggtgaatatg caaggcggta cactacgcac tggacagcat cagaaatcct ctgttaatgt 1740ggactggaac atggtagatg cttgattgtt ttggtctcaa aatggtgtgc tataaagata 1800aaggtgaggg gaagacaaag cacaccatat gtccactgtt ctgttctcat agaggaaatt 1860caaatccctt ttatctatta gataatcaag ggcactgtga tacagttttg agtaaaaaga 1920cattttttaa aagccttcca gttttgtgga ttaaaccttt ttataaagat catttataat 1980actgttttaa aatgtgaggc aataagaatt actttgtgtt ggatctgagg aggctttggt 2040aaaacagttt catctaaatg aaagtggtaa tcctcttcta aaatagcaat aactgaaaat 2100gaaagtgtta attttacctt gtttgagtta tcagggaact tagtaagtaa tatcaaagca 2160ttttataaat gatatcaaag aagagtcaac attgatccag tcattttatt ttgtaatatt 2220gagggataat tggttattaa actgaatagt tcaggagact ttacaaacct ttgtttcaac 2280tttcttatct ggaaataata tcatttataa agggacactt ttatgttttt ccctttttta 2340tgttggttga tataacacaa agagatattt aggaaaatgc ttattgatga ggtttattct 2400atctgttttt aaagcaccga ggttgcattc tagataacct tgtttattag catggcatat 2460tttaatcatt atttgagact gtcctgtgcc tgattatttt agctaaattc agggagattg 2520cgtggggcag gaaagcatgc attgaaaaat ttctaaccac ggttatttaa gcataatctg 2580aaaacatcta gcccaaaggt aagttgctat tttcatcaca gttgcctatg cccagggaat 2640aagatgtatt ctttataatt gaattggttt ttcccacgtc taactggaaa caaaacagaa 2700ggggcgtcat aaatttgaat aagcagaaca tactgttctc aacatactgt aatcaaaagg 2760aggaatttca gtgggtctct gtgtgtgtat gagagagaga gtgtgtgttt gtgtgtttca 2820aggtcagaac aggttttttt gtttttgttt tttgttcttt gttttttttt ttgagatgga 2880gtcttgctct tgtcgcccag gctggagtgc agtggcgcaa tctcagctca ctgcaacctc 2940cgcctcccag gttcaagcag ttctcctgcc tcagcctcct gagtagctgg gatgacaggc 3000acccgccacc acacccagct aatttttgta cttttagtag agacgaggtt tcgccatgtt 3060ggccaggctg gtctcgaact cctgacctca ggtgatccac ccgcctcggc cttccaaagt 3120gctgggatta caggcgtgag ccaccgtgcc tggccagaat aggttttttc tttcaacttg 3180atcagtagaa aatggacatc aagtttgaac agataaatca tggacagcct tattgtgatt 3240gaaatgcttg taggttctgt gccaattttc caccactgtg tactttgttg ctatttaaaa 3300ctgtatcaac tctaacggaa gaataaatta tttgtgattt taaaaaa 334764903DNAHomo sapiens 6gtcgtttgcg gcggcgcagg cgcggtgcgg gcggcggacg ggcgggcgct tcgccgtttg 60aatggctgcg ggcccgggcc ctcacctcac ctgaggtccg gccgcccagg ggtgcgctat 120gccgtcggga ggtgaccagt cgccaccgcc cccgcctccc cctccggcgg cggcagcctc 180ggatgaggag gaggaggacg acggcgaggc ggaagacgcc gcgccgcctg ccgagtcgcc 240cacccctcag atccagcagc ggttcgacga gctgtgcagc cgcctcaaca tggacgaggc 300ggcgcgggcc gaggcctggg acagctaccg cagcatgagc gaaagctaca cgctggaggg 360aaatgatctt cattggttag catgtgcctt atatgtggct tgcagaaaat ctgttccaac 420tgtaagcaaa gggacagtgg aaggaaacta tgtatcttta actagaatcc tgaaatgttc 480agagcagagc ttaatcgaat tttttaataa gatgaagaag tgggaagaca tggcaaatct 540acccccacat ttcagagaac gtactgagag attagaaaga aacttcactg tttctgctgt 600aatttttaag aaatatgaac ccatttttca ggacatcttt aaataccctc aagaggagca 660acctcgtcag cagcgaggaa ggaaacagcg gcgacagccc tgtactgtgt ctgaaatttt 720ccatttttgt tgggtgcttt ttatatatgc aaaaggtaat ttccccatga ttagtgatga 780tttggtcaat tcttatcacc tgctgctgtg tgctttggac ttagtttatg gaaatgcact 840tcagtgttct aatcgtaaag aacttgtgaa ccctaatttt aaaggcttat ctgaagattt 900tcatgctaaa gattctaaac cttcctctga ccccccttgt atcattgaga aactgtgttc 960cttacatgat ggcctagttt tggaagcaaa ggggataaag gaacatttct ggaaacccta 1020tattaggaaa ctttatgaaa aaaagctcct taagggaaaa gaagaaaatc tcactgggtt 1080tctagaacct gggaactttg gagagagttt taaagccatc aataaggcct atgaggagta 1140tgttttatct gttgggaatt tagatgagcg gatatttctt ggagaggatg ctgaggagga 1200aattgggact ctctcaaggt gtctgaacgc tggttcagga acagagactg ctgaaagggt 1260gcagatgaaa aacatcttac agcagcattt tgacaagtcc aaagcactta gaatctccac 1320accactaact ggtgttaggt acattaagga gaatagccct tgtgtgactc cagtttctac 1380agctacgcat agcttgagtc gtcttcacac catgctgaca ggcctcagga atgcaccaag 1440tgagaaactg gaacagattc tcaggacatg ttccagagat ccaacccagg ctattgctaa 1500cagactgaaa gaaatgtttg aaatatattc tcagcatttc cagccagacg aggatttcag 1560taattgtgct aaagaaattg ccagcaaaca ttttcgtttt gcggagatgc tttactataa 1620agtattagaa tctgttattg agcaggaaca aaaaagacta ggagacatgg atttatctgg 1680tattctggaa caagatgcgt tccacagatc tctcttggcc tgctgccttg aggtcgtcac 1740tttttcttat aagcctcctg ggaattttcc atttattact gaaatatttg atgtgcctct 1800ttatcatttt tataaggtga tagaagtatt cattagagca gaagatggcc tttgtagaga 1860ggtggtaaaa caccttaatc agattgaaga acagatctta gatcatttgg catggaaacc 1920agagtctcca ctctgggaaa aaattagaga caatgaaaac agagttccta catgtgaaga 1980ggtcatgcca cctcagaacc tggaaagggc agatgaaatt tgcattgctg gctccccttt 2040gactcccaga agggtgactg aagttcgtgc tgatactgga ggacttggaa ggagcataac 2100atctccaacc acattatacg ataggtacag ctccccacca gccagcacta ccagaaggcg 2160gctatttgtt gagaatgata gcccctctga tggagggacg cctgggcgca tgcccccaca 2220gcccctagtc aatgctgtcc ctgtgcagaa tgtatctggg gagactgttt ctgtcacacc 2280agttcctgga cagactttgg tcaccatggc aaccgccact gtcacagcca acaatgggca 2340aacggtaacc attcctgtgc aaggtattgc caatgaaaat ggagggataa cattcttccc 2400tgtccaagtc aatgttgggg ggcaggcaca agctgtgaca ggctccatcc agcccctcag 2460tgctcaggcc ctggctggaa gtctgagctc tcaacaggtg acaggaacaa ctttgcaagt 2520ccctggtcaa gtggccattc aacagatttc cccaggtggc caacagcaga agcaaggcca 2580gtctgtaacc agcagtagta atagacccag gaagaccagc tctttatcgc ttttctttag 2640aaaggtatac catttagcag ctgtccgcct tcgggatctc tgtgccaaac tagatatttc 2700agatgaattg aggaaaaaaa tctggacctg ctttgaattc tccataattc agtgtcctga 2760acttatgatg gacagacatc tggaccagtt attaatgtgt gccatttatg tgatggcaaa 2820ggtcacaaaa gaagataagt ccttccagaa cattatgcgt tgttatagga ctcagccgca 2880ggcccggagc caggtgtata gaagtgtttt gataaaaggg aaaagaaaaa gaagaaattc 2940tggcagcagt gatagcagaa gccatcagaa ttctccaaca gaactaaaca aagatagaac

3000cagtagagac tccagtccag ttatgaggtc aagcagcacc ttgccagttc cacagcccag 3060cagtgctcct cccacaccta ctcgcctcac aggtgccaac agtgacatgg aagaagagga 3120gaggggagac ctcattcagt tctacaacaa catctacatc aaacagatta agacatttgc 3180catgaagtac tcacaggcaa atatggatgc tcctccactc tctccctatc catttgtaag 3240aacaggctcc cctcgccgaa tacagttgtc tcaaaatcat cctgtctaca tttccccaca 3300taaaaatgaa acaatgcttt ctcctcgaga aaagattttc tattacttca gcaacagtcc 3360ttcaaagaga ctgagagaaa ttaatagtat gatacgcaca ggagaaactc ctactaaaaa 3420gagaggaatt cttttggaag atggaagtga atcacctgca aaaagaattt gcccagaaaa 3480tcattctgcc ttattacgcc gtctccaaga tgtagctaat gaccgtggtt cccactgagg 3540ttagtctctt gtattaaact cttcacaaaa tctgtttagc agcagccttt aatgcatcta 3600gattatggag cttttttcct taatccagct gatgagttac agcctgttag taacatgagg 3660ggacattttg gtgagaaatg ggacttaact ccttccagtg tccttagaac attttaattc 3720atcccaactg tctttttttc cctaccattc agtgattact gtcaaggctg cttagaatcc 3780aaacttggat ttttgactct ggcaaagctt ttagaaatac tgcaagaaaa tgatgtgtac 3840ccaaacgtga gcataggagg cttctgttga cgtactccaa cagaagaact gtgtttcaag 3900ttcaatccta cctgttttgt ggtcagctgt agtcctcata aaaagcaaaa caaaaattag 3960gtattttgtc ctaaaacacc tggtaggagt gtgtgatttt ttgcattcct gacaaaggag 4020agcacaccca ggtttggagg tcctaggtca ttagccctcg tctcccgttc cctttgtgca 4080catcttccct ctccccattc ggtgtggtgc agtgtgaaaa gtccttgatt gttcgggtgt 4140gcaatgtctg agtgaacctg tataagtgga ggcactttag ggctgtaaaa tgcatgattt 4200tgtaacccag attttgctgt atatttgtga tagcactttc tacaatgtga actttattaa 4260atacaaaact tccaggctaa acatccaata ttttctttaa tgcttttata tttttttaaa 4320atgttaaaac ccctatagcc accttttggg aatgttttaa attctccagt tttttgttat 4380atagggatca accagctaag aaaagatttt aatcaagttg aattgagggg attaatatga 4440aaacttatga cctcttcctt taggagggag ttatctaaaa gaaatgtcta ttaaggtgat 4500atatttaaaa atatttttgg gtgttcctgg cagtttaaaa aaattggttg gagaatttag 4560gtttttatta gtaccatagt accatttata caaattagaa aatgttattt aacagctgaa 4620ttatctatac atatctttat taatcactat tgttccagca gttttcaagt caaattaata 4680atcttattag ggagaaaatt caattgtaaa ttgaatcagt ataaacaaag ttactaggta 4740acttcatatt gctgagagaa atatggaact tacattgttc aattagaata gtgttctgca 4800aaaatattta taaaacttct caagatactg ctactgtaat tttatatgaa gataagtgta 4860tttttcaata aagcatttat aaattaaaaa aaaaaaaaaa aaa 490373324DNAHomo sapiens 7agtgccacag gcaaccctgc acgtgacgct tgcggaggaa ggggagagag aggcgcgcgg 60gagggcgtct agggaatcga ggtgccggct gctccttcct cacaatttgg tttgtgctgc 120aaggggaggg tccccatcat ctggccccag tggtgtaagg agctgactgg gattcagtca 180ctgacttgga gccgctcggg ggaagtcccg cccagacagg cggtgggtgg gaatgcctca 240cttcagtttg aagagggtcc ggatccaaag gggttaaaac gagcgacccc cgatccccga 300ccacacttcc cgcctcccta aaacgcacac cccgctagcc atgggcagcc gcgaccacct 360gttcaaagtg ctggtggtgg gggacgccgc agtgggcaag acgtcgctgg tgcagcgata 420ttcccaggac agcttcagca aacactacaa gtccacggtg ggagtggatt ttgctctgaa 480ggttctccag tggtctgact acgagatagt gcggcttcag ctgtgggata ttgcagggca 540ggagcgcttc acctctatga cacgattgta ttatcgggat gcctctgcct gtgttattat 600gtttgacgtt accaatgcca ctaccttcag caacagccag aggtggaaac aggacctaga 660cagcaagctc acactaccca atggagagcc ggtgccctgc ctgctcttgg ccaacaagtg 720tgatctgtcc ccttgggcag tgagccggga ccagattgac cggttcagta aagagaacgg 780tttcacaggt tggacagaaa catcagtcaa ggagaacaaa aatattaatg aggctatgag 840agtcctcatt gaaaagatga tgagaaattc cacagaagat atcatgtctt tgtccaccca 900aggggactac atcaatctac aaaccaagtc ctccagctgg tcctgctgct agtagtgttt 960ggcttatttt ccatcccagt tctgggaggt cttttaagtc tcttcccttt ggttgcccac 1020ctgacaattt tattaagtac atttgaattg tctcctgact actgtccagt aaggaggccc 1080attgtcactt agaaaagaca cctggaaccc atgtgcattt ctgcatctcc tggattagcc 1140tttcacatgt tgctggctca cattagtgcc agttagtgcc ttcggtgtaa gatcttctca 1200tcagccctca atttgtgatc cggaatttta tgagaaggat tagaaatcag cacctgcgtt 1260ttagagatca taattctcac ctacttctga gcttattttt ccatttgata ttcattgata 1320tcatgacttc caattgagag gaaaatgaga tcaaatgtca tttcccaaat ttcttgtagg 1380ccgttgtttc agattctttc tgtcttggaa tgtaaacatc tgattctgga atgcagaagg 1440agggggtctg ggcatctgtg gatttttggc tactagaagt gtcccagaag tcactgtatt 1500tttgaaactt ctaacgtcat aattaagttt ctcttgtctt ggcatcaaga atagtcaagt 1560tttttggccg ggcatggtgg ctcatgcctg taatcccagc acttggggag gccaaggcag 1620gcggatcaca tgaggccagg aattcgagac caacctggtc agcatggcaa aaccccgtct 1680ctactaaaag tacaaaaatt agccaggcgt gatggcacgt gtctgtaatc ccagctactc 1740tggagactga ggtgggagaa tcgcttgaga ctgggaggca gaggttgcag tgaaccgaga 1800tcatgccacc gcacttcagc ctgggtgaca gagaaggact ccgtctcaaa aaaaaaagaa 1860aaaagaatag tcatttttaa actacctatc tcatgcaatg aaagcatttt cttccacaaa 1920gagcttaatc ctcatgatag gattgcctag tgtctcccat ttgcaggttt ctgggttgat 1980gtcttaatgc ataatactgc aagtgacatc agctggctgt gatgcttcga aataggtctg 2040ctcctcacag ctttgggaat ctgaatggaa gaagaaaaga gagaagttaa caacctccac 2100tggggcaact ttgtgaacac gtaggcactt agtcatagga aacatattat gtgcaggtcc 2160tagcctgggg gaggaaagta gatagacaga aaatcattag gtaatttaag tactaaattg 2220ggcagggctt tttagtatca aatcactact agaccattta atttgttaaa ttatctctag 2280gatggtgatt tataacctac ccaaagttat cgatattctt actaaactct gaggcctgaa 2340gttctgtgat agaccttaaa taagtgtcct aagtcagtgg ttcccaaatc tggctggtcg 2400ggaatacctg ggaagtttgt taaaattttt taaaaatgtt ttaagatttt tgggtcctga 2460gccagccgtg gtggctcaca cctgtaatcc cagcactttg ggaggctgag gcaggtggat 2520cgcctgaggt caggagttca agatcaacct ggccaacata ctgaaacccc gtctctacta 2580aaaataagaa aaattagctg ggcgtggtgg cgggcacctg taatcccagc tacttgggag 2640actgaggcag gagaatcgct tgaacctggg agttagaggt tgcagtgagc tgagatcaca 2700ccattgcgct tcagcctggg caacaagagt gaaactccat ctccaaaaaa aaaaaacaaa 2760aagaaaaaga tttttgggtc ccgacctcaa acctactgaa tcagaatttc tagggatgaa 2820gcctaggaat gtgttgttgt tttcagagct tccctggtga ttgtgataag cctggtttgg 2880aaaccattgc tggagaactt tgtaaagata cagagaccca gaccttttgt atttacattt 2940aaatacaaat acaaatcctg ggtttctata tattctgtta gcttttcagg tgattctgct 3000acacagacgt tgaaaaccac tgccctaaga aagagatcag aggccacata tcagagagaa 3060aagggaccaa accttcggtg gtttgttgtg tgtcgtttta atgccaatta ttttaacttg 3120cacagtcttc tgaaaccttg tattaatagt tctcttttgt attaccattt tcaggtaggg 3180ttttgatcac tatgattctg aagataatag tgaaatagtg aatttcattg atatgaagag 3240ataattgatt ttcattcatt ggtttgaaca cctgcaaaat cacaaataaa tgagaactaa 3300gtcttgtaaa aaaaaaaaaa aaaa 332483466DNAHomo sapiens 8aattacggcc ggattccgga gtcctttcca gctccctctt cggccgggtt tcccgccgaa 60tacaaaggcg cactgtgaac tggctctttc tttccgccaa tcatttccgc cagccattca 120tcaccgattt tcttcatctt cccctccctc ttccgtcccg cagtccccga cctgttagct 180ctcggttagt taagggactc gggtccttcc gaactgcgca tgcgccaccg cgtctgcagg 240gggagaagcg ggcaggggcg caggcgcagt agtgtgatcc cctggccagt ccctaagcac 300gtgggttggg ttgtcctgct tggctgcgga gggagtggaa cctcgatatt ggtggtgtcc 360atcgtgggca gcggactaat aaaggccatg gcgccagcag aaatcctgaa cgggaaggag 420atctccgcgc aaataagggc gagactgaaa aatcaagtca ctcagttgaa ggagcaagta 480cctggtttca caccacgcct ggcaatatta caggttggca acagagatga ttccaatctt 540tatataaatg tgaagctgaa ggctgctgaa gagattggga tcaaagccac tcacattaag 600ttaccaagaa caaccacaga atctgaggtg atgaagtaca ttacatcttt gaatgaagac 660tctactgtac atgggttctt agtgcagcta cctttagatt cagagaattc cattaacact 720gaagaagtga tcaatgctat tgcacccgag aaggatgtgg atggattgac tagcatcaat 780gctgggaaac ttgctagagg tgacctcaat gactgtttca ttccttgtac gcctaaggga 840tgcttggaac tcatcaaaga gacaggggtg ccgattgccg gaaggcatgc tgtggtggtt 900gggcgcagta aaatagttgg ggccccgatg catgacttgc ttctgtggaa caatgccaca 960gtgaccacct gccactccaa gactgcccat ctggatgagg aggtaaataa aggtgacatc 1020ctggtggttg caactggtca gcctgaaatg gttaaagggg agtggatcaa acctggggca 1080atagtcatcg actgtggaat caattatgtc ccagatgata aaaaaccaaa tgggagaaaa 1140gttgtgggtg atgtggcata cgacgaggcc aaagagaggg cgagcttcat cactcctgtt 1200cctggcggcg tagggcccat gacagttgca atgctcatgc agagcacagt agagagtgcc 1260aagcgtttcc tggagaaatt taagccagga aagtggatga ttcagtataa caaccttaac 1320ctcaagacac ctgttccaag tgacattgat atatcacgat cttgtaaacc gaagcccatt 1380ggtaagctgg ctcgagaaat tggtctgctg tctgaagagg tagaattata tggtgaaaca 1440aaggccaaag ttctgctgtc agcactagaa cgcctgaagc accggcctga tgggaaatac 1500gtggtggtga ctggaataac tccaacaccc ctgggagaag ggaaaagcac aactacaatc 1560gggctagtgc aagcccttgg tgcccatctc taccagaatg tctttgcgtg tgtgcgacag 1620ccttctcagg gccccacctt tggaataaaa ggtggcgctg caggaggcgg ctactcccag 1680gtcattccta tggaagagtt taatctccac ctcacaggtg acatccatgc catcactgca 1740gctaataacc tcgttgctgc ggccattgat gctcggatat ttcatgaact gacccagaca 1800gacaaggctc tctttaatcg tttggtgcca tcagtaaatg gagtgagaag gttctctgac 1860atccaaatcc gaaggttaaa gagactaggc attgaaaaga ctgaccctac cacactgaca 1920gatgaagaga taaacagatt tgcaagattg gacattgatc cagaaaccat aacttggcaa 1980agagtgttgg ataccaatga tagattcctg aggaagatca cgattggaca ggctccaacg 2040gagaagggtc acacacggac ggcccagttt gatatctctg tggccagtga aattatggct 2100gtcctggctc tcaccacttc tctagaagac atgagagaga gactgggcaa aatggtggtg 2160gcatccagta agaaaggaga gcccgtcagt gccgaagatc tgggggtgag tggtgcactg 2220acagtgctta tgaaggacgc aatcaagccc aatctcatgc agacactgga gggcactcca 2280gtgtttgtcc atgctggccc gtttgccaac atcgcacatg gcaattcctc catcattgca 2340gaccggatcg cactcaagct tgttggccca gaagggtttg tagtgacgga agcaggattt 2400ggagcagaca ttggaatgga aaagtttttt aacatcaaat gccggtattc cggcctctgc 2460ccccacgtgg tggtgcttgt tgccactgtc agggctctca agatgcacgg gggcggcccc 2520acggtcactg ctggactgcc tcttcccaag gcttacatac aggagaacct ggagctggtt 2580gaaaaaggct tcagtaactt gaagaaacaa attgaaaatg ccagaatgtt tggaattcca 2640gtagtagtgg ccgtgaatgc attcaagacg gatacagagt ctgagctgga cctcatcagc 2700cgcctttcca gagaacatgg ggcttttgat gccgtgaagt gcactcactg ggcagaaggg 2760ggcaagggtg ccttagccct ggctcaggcc gtccagagag cagcacaagc acccagcagc 2820ttccagctcc tttatgacct caagctccca gttgaggata aaatcaggat cattgcacag 2880aagatctatg gagcagatga cattgaatta cttcccgaag ctcaacacaa agctgaagtc 2940tacacgaagc agggctttgg gaatctcccc atctgcatgg ctaaaacaca cttgtctttg 3000tctcacaacc cagagcaaaa aggtgtccct acaggcttca ttctgcccat tcgcgacatc 3060cgcgccagcg ttggggctgg ttttctgtac cccttagtag gaacgatgag cacaatgcct 3120ggactcccca cccggccctg tttttatgat attgatttgg accctgaaac agaacaggtg 3180aatggattat tctaaacaga tcaccatcca tcttcaagaa gctactttga aagtctggcc 3240agtgtctatt caggcccact gggagttagg aagtataagt aagccaagag aagtcagccc 3300ctgcccagaa gatctgaaac taatagtagg agtttcccca gaagtcattt tcagccttaa 3360ttctcatcat gtataaatta acataaatca tgcatgtctg tttactttag tgacgttcca 3420cagaataaaa ggaaacaagt ttgccatcaa aaaaaaaaaa aaaaaa 346692543DNAHomo sapiens 9caatttttaa gaaatgatca tctagggaaa atgttttaaa atcttttaaa atatcttttt 60gttatacttt aaaactgcct tcagctgcct attggtaaat aaggtctgga tatcagtaca 120tgacaacata tactaatgaa ttgaactgtg aattaggaat gaaaattgcc tagaaatttt 180tttatgagtt attaggatta aagtaagaat ttcctttgct gggctgtgta ggcactaaga 240ttccgtggtt gttggagggg ttaaatttgg atctactagt gcatatattt taccgaggat 300tcataaaaac acgacagtgg agcctgggtc aatccattac catgtacaag cagtgaccaa 360tagaaaagga agaagaagat ccaagaaggc tgaggtaagc agtcttctga agccctgtca 420aagtggaaac aatagatcaa aggtgttcat ggtgactggg acgagtaggt ttcactgttt 480ctcataggag acttgacagc ttaaagtaaa aacaaattat tttcgtcaaa gttttttttt 540ttctcttaac tgatttttag caaacctcag actgagacac aggactcaac ggtgtattcc 600tggaaggcaa ggtgctataa tggcaggcac aatctgtttc atcatgtggg tgttattcat 660aacagacact gtgtggtcta gaagtgtgag gcaggtctat gaagtacatg attcagatga 720ttggactatt catgacttcg agtgtcccat ggaatgtttc tgcccaccca gttttcctac 780tgctttatat tgtgaaaata gaggtctcaa agaaattcct gctattcctt caagaatttg 840gtatctttat cttcaaaaca acctgataga aaccattcct gaaaagccat ttgagaatgc 900cacccagcta agatggataa atctaaacaa gaacaaaata accaactacg gaattgaaaa 960aggagcccta agccagctga agaagttgct cttcttattt ctggaagata atgagctaga 1020ggaggtacct tctccattgc caagaagttt agaacaatta caattagcta gaaataaggt 1080gtccagaatt cctcaaggga cctttagcaa tctggagaac ctgacccttc ttgacctaca 1140gaacaacaaa ttagtggaca atgcctttca aagagacact tttaaaggac tcaagaatct 1200catgcagcta aacatggcca agaatgccct gaggaatatg cctccaagat taccagccaa 1260tacaatgcag ttgtttttag acaacaattc cattgaagga ataccagaaa attattttaa 1320tgtgattcct aaagtggcct ttttgagact aaatcacaac aaactgtcag atgagggtct 1380cccatcaaga ggatttgatg tatcatcaat tctagatctt caactgtcgc acaatcaact 1440cacaaaggtt ccccgaatca gtgctcatct gcagcacctt caccttgatc ataacaaaat 1500taaaagtgtg aatgtctctg taatatgtcc cagcccatcc atgctgcctg cagaacgaga 1560ttccttcagt tatggacctc atcttcgcta cctccgtctg gatggaaatg aaatcaaacc 1620accaattcca atggctttaa tgacctgctt cagacttctg caggctgtca ttatttaaac 1680acattctcac caaatctaaa attagtttaa tgagctgttt ctgacatgaa atgtggttac 1740cattaatagg tttaggacac aagtcatatt ccccattgct ctcggccacc attttcattt 1800gtgcagtgta ttttttctat tcaaagatgc ttttgccagt tacatgcatc acagcctgca 1860ttaatttgct tttcttttaa ttaataaaac agacacagag ttaagatagt ttatcaactc 1920aaagatagtt ttattttggt ctcttccata gcttattaac actaaagaaa acaattacat 1980tcttatacaa taaaaaggac acatttgtgt atgtttaaaa ttacttatgc agataccgta 2040atttacagta taaatgtaat aatcaaacag gaggataacg acctgaagaa aatgagaaaa 2100taaaatattt cttaattgta atcataataa aacaattgca gattgctaag tagctgttgg 2160tggtacaagt ttgatattta gcttgagaat gggtatggaa tgaatcaaat acttcatcac 2220taaagaattc ttgttattta atatcaaata atgaaacagc agtcacttct agttcattac 2280catttcttgt agctgttgtt tttagatata gtccactgca ttcttataag ttctaaattt 2340tatgtttatt ataatgcatt tcttgtggaa tcttagtgtt ttaacatttg aaatccactt 2400aaactgcaaa ttgttcttta tatttgattg tgttttttgg attttctaaa taaaaatatt 2460gaatgctttc taacaaaaca gaatatttca aagaaattag caagcttcat taaagaacat 2520gttttaataa aaaaaaaaaa aaa 2543103435DNAHomo sapiens 10acagcaacta tgaaataatc gtagtatgag aggcagagat cggggcgaga caatggggat 60gtgggcgcgg gagccccgtt ccggcttagc agcacctccc agccccgcag aataaaaccg 120atcgcgcccc ctccgcgcgc gccctccccc gagtgcggag cgggaggagg cggcggcggc 180cgaggaggag gaggaggagg ccccggagga ggaggcgttg gaggtcgagg cggaggcgga 240ggaggaggag gccgaggcgc cggaggaggc cgaggcgccg gagcaggagg aggccggccg 300gaggcggcat gagacgagcg tggcggccgc ggctgctcgg ggccgcgctg gttgcccatt 360gacagcggcg tctgcagctc gcttcaagat ggccgcttgg ctcgcattca ttttctgctg 420aacgactttt aactttcatt gtcttttccg cccgcttcga tcgcctcgcg ccggctgctc 480tttccgggat tttttatcaa gcagaaatgc atcgaacaac gagaatcaag atcactgagc 540taaatcccca cctgatgtgt gtgctttgtg gagggtactt cattgatgcc acaaccataa 600tagaatgtct acattccttc tgtaaaacgt gtattgttcg ttacctggag accagcaagt 660attgtcctat ttgtgatgtc caagttcaca agaccagacc actactgaat ataaggtcag 720ataaaactct ccaagatatt gtatacaaat tagttccagg gcttttcaaa aatgaaatga 780agagaagaag ggatttttat gcagctcatc cttctgctga tgctgccaat ggctctaatg 840aagatagagg agaggttgca gatgaagata agagaattat aactgatgat gagataataa 900gcttatccat tgaattcttt gaccagaaca gattggatcg gaaagtaaac aaagacaaag 960agaaatctaa ggaggaggtg aatgataaaa gatacttacg atgcccagca gcaatgactg 1020tgatgcactt aagaaagttt ctcagaagta aaatggacat acctaatact ttccagattg 1080atgtcatgta tgaggaggaa cctttaaagg attattatac actaatggat attgcctaca 1140tttatacctg gagaaggaat ggtccacttc cattgaaata cagagttcga cctacttgta 1200aaagaatgaa gatcagtcac cagagagatg gactgacaaa tgctggagaa ctggaaagtg 1260actctgggag tgacaaggcc aacagcccag caggaggtat tccctccacc tcttcttgtt 1320tgcctagccc cagtactcca gtgcagtctc ctcatccaca gtttcctcac atttccagta 1380ctatgaatgg aaccagcaac agccccagcg gtaaccacca atcttctttt gccaatagac 1440ctcgaaaatc atcagtaaat gggtcatcag caacttcttc tggttgatac ctgagactgt 1500taaggaaaaa aattttaaac ccctgattta tatagatatc ttcatgccat tacagctttc 1560tagatgctaa tacatgtgac tatcgtccaa tttgctttct tttgtagtga cattaaattt 1620ggctataaaa gatggactac atgtgatact cctatggacg ttaattgaaa agaaagattg 1680ttgttataaa gaattggttt cttggaaagc aggcaagact ttttctctgt gttaggaaag 1740atgggaaatg gtttctgtaa ccattgtttg gatttggaag tactctgcag tggacataag 1800cattgggcca tagtttgtta atctcaacta acgcctacat tacattctcc ttgatcgttc 1860ttgttattac gctgttttgt gaacctgtag aaaacaagtg ctttttatct tgaaattcaa 1920ccaacggaaa gaatatgcat agaataatgc attctatgta gccatgtcac tgtgaataac 1980gatttcttgc atatttagcc attttgattc ctgtttgatt tatacttctc tgttgctacg 2040caaaaccgat caaagaaaag tgaacttcag ttttacaatc tgtatgccta aaagcgggta 2100ctaccgttta ttttactgac ttgtttaaat gattcgcttt tgtaagaatc agatggcatt 2160atgcttgttg tacaatgcca tattggtata tgacataaca ggaaacagta ttgtatgata 2220tatttataaa tgctataaag aaatattgtg tttcatgcat tcagaaatga ttgttaaaat 2280tctcccaact ggttcgacct ttgcagatac ccataaccta tgttgagcct tgcttaccag 2340caaagaatat ttttaatgtg gatatctaat tctaaagtct gttccattag aagcaattgg 2400cacatctttc tatactttat atacttttct ccagtaatac atgtttactt taaagattgt 2460tgcagtgaag aaaaaccttt aactgagaaa tatggaaacc gtcttaattt tccattggct 2520atgatggaat taatattgta ttttaaaaat gcatattgat cactataatt ctaaaacaat 2580tttttaaata aaccagcagg ttgctaaaag aaggcatttt atctaaagtt attttaatag 2640gtggtatagc agtaatttta aatttaagag ttgcttttac agttaacaat ggaatatgcc 2700ttctctgcta tgtctgaaaa tagaagctat ttattatgag cttctacagg tatttttaaa 2760tagagcaagc atgttgaatt taaaatatga ataaccccac ccaacaattt tcagtttatt 2820ttttgctttg gtcgaacttg gtgtgtgttc atcacccatc agttatttgt gagggtgttt 2880attctatatg aatattgttt catgtttgta tgggaaaatt gtagctaaac atttcattgt 2940ccccagtctg caaaagaagc acaattctat tgctttgtct tgcttatagt cattaaatca 3000ttacttttac atatattgct gttacttctg ctttctttaa aaatatagta aaggatgttt 3060tatgaagtca caagatacat atatttttat tttgacctaa atttgtacag tcccattgta 3120agtgttgttt ctaattatag atgtaaaatg aaatttcatt tgtaattgga aaaaatccaa 3180taaaaaggat attcatttag aaaatagcta agatctttaa taaaaatttg atatgaaaag 3240cacaatgtgc agaagttatg gaaaacctat agaggattac aacaggtaaa cgttaaagag 3300aatacattgc tgacttatag tgatgtggct aagaagtaca tgctttgttg taaaattgct 3360tgaaagccca ttgaaagatg tatctgttta tttacagtct ttgaagtaaa agttaccaat 3420gtttgccaat aaaaa 3435114880DNAHomo sapiens 11attggtcctt ttatggttca gacttccttc ttcatcgact ctccctaatt ctcttcactg 60ttcatcccca gcaacttttc ttcccaagca tttcctgcgg gcttttatta ccccaggagt 120gccaatcaag gcgtggaaca

gataaagctg tgtagcaact aacgcgtgac tcttgtgagt 180gtggagggca aacgaagctc cctgaaacct ccgctctgct ctcctgcctt acgccgcgcg 240gcccctgttc tgaggtttaa tacttgcttc acagataagc gctgcggcca cgttccggtg 300cccaccttct ccttggctag ggcacgacgc cagcccaggg ggcgcggccc tgagctgctg 360cgagagacag ctgaaagcgc cggcccgacg gccttggctc cctcggtgcg ctgggcgcag 420agcactcgga ccctgggcgc ccactgctcg agtacctgcg cggctcctag ccaggcttag 480cccaggcgcg ggctgagagt cagttcgcca ggtgggcctg gagccatggg ctgggtgggc 540gggcggcgcc gggattctgc gtcaccacct gggcggagcc gttctgctgc tgacgacatc 600aacccggcac ctgccaacat ggaaggtggc ggcggcagcg tcgctgtagc tggcctcgga 660gctcgaggct ctggagcggc tgcagctaca gtccgggaac ttctgcagga cgggtgttat 720agtgactttt taaacgaaga ctttgatgta aagacttata cttctcaatc tattcatcaa 780gctgtaattg ctgaacaact agcaaaactt gcccaaggaa tcagtcagtt ggacagagaa 840ctacacttac aggttgttgc aagacatgaa gatttactgg cacaagcaac tgggattgag 900tcgttggaag gtgttcttca gatgatgcag acgagaattg gggctttaca gggagctgtt 960gataggataa aagcaaaaat tgttgaacca tacaataaga tagttgcccg gactgcacaa 1020ctagcaagac ttcaggttgc ctgtgatttg cttcggagga ttattcgtat cttgaatctc 1080agtaagagac tccaaggaca actgcaaggg ggaagtagag agataacaaa agctgctcag 1140agtctcaatg aacttgatta tctttctcaa ggaatagatc tttctggaat agaagtgata 1200gaaaatgatc tactttttat tgcaagagcc cgacttgaag tggaaaatca agctaagcgc 1260ctactagagc agggtttgga gactcagaat ccaactcaag tcggaacagc tcttcaggtt 1320ttctataatc ttggaacttt gaaggatact attaccagtg ttgtggatgg atattgtgct 1380actttagaag aaaatatcaa cagtgcatta gacataaaag ttttgactca gccttcccag 1440tcagctgtga gagggggacc tggacgatct accatgccaa ccccaggaaa tactgcagct 1500ttgcgtgcct cattctggac caatatggag aaacttatgg atcatattta tgctgtttgt 1560ggacaggtac aacatctaca aaaagtattg gccaagaaga gagatcctgt ttctcacatt 1620tgtttcattg aagaaatagt taaggatgga caaccggaaa ttttctacac attttggaat 1680tcagttactc aggcactttc ttctcaattt catatggcaa caaactcttc gatgtttttg 1740aagcaggcat ttgaaggaga ataccctaaa ttattacgtc tttataatga cttatggaag 1800cgtcttcaac aatacagtca gcatatccaa gggaatttta atgcaagtgg aactacagac 1860ctctatgttg acctacaaca catggaagat gatgcacaag atatattcat accaaaaaag 1920ccagattatg atccagaaaa ggctttgaaa gactcactac aaccctatga ggctgcttat 1980ctatcaaaat ccttatctcg actcttcgat cctatcaact tggtttttcc cccgggtggt 2040cgtaatcctc cttcctctga tgaacttgat ggtattatta aaactatagc aagtgaacta 2100aatgttgctg ctgttgatac aaacctcaca ttagctgtgt caaaaaatgt ggcaaagacc 2160atccagttat acagtgtaaa atcagagcag cttctctcca cacaaggaga tgcaagtcag 2220gtgattgggc ctcttactga aggacagaga agaaatgtgg cagtagtgaa ttcattgtat 2280aagttgcacc aatcagtaac aaaggttgtt tccagtcaga gctcattccc actggcagct 2340gagcaaacta taatttcagc tctaaaggct attcatgctc ttatggaaaa tgctgtgcaa 2400cccttactca cttctgtggg agatgctata gaggccataa tcatcaccat gcatcaagaa 2460gacttttctg ggtcattatc cagctcagga aaacctgatg ttccttgttc tctgtacatg 2520aaggagctac aaggtttcat tgccagagtt atgagtgact attttaaaca ctttgaatgc 2580ttggattttg tctttgacaa cactgaggct attgcccaaa gagctgttga actttttatc 2640cgccatgcca gtctcataag acctcttggt gaaggtggga aaatgcgact tgctgctgat 2700tttgcacaga tggagttggc tgtgggtcca ttctgtagac gagtatctga tttaggaaag 2760tcctatcgga tgctgagatc attcagacct ctgctcttcc aggcaagtga acatgtagcc 2820agtagtcctg cattggggga tgtgattccg ttcagcatca ttattcagtt tttgttcacg 2880agagcacccg ctgaactgaa atctcctttc cagagggcag agtggtccca cacacgcttc 2940tctcagtggc tggatgacca tccatctgaa aaggacaggc tcctcctcat caggggagcc 3000ctggaagctt atgttcaatc agtgagaagt agagaaggca aagaatttgc accagtttat 3060cccataatgg ttcagctgct tcaaaaggct atgtctgctc ttcagtaatg acatgaaatc 3120tttgttcatc tccactttgt gctaacccat tcatagttgg cagttaaaca catactccaa 3180aagactgcta ctatctacta ttttaagaat gtaattgatt gttcggtatt tcctatcgac 3240gtttatttac ctctttagca cttatacttt agcataaaaa atgttgagtt atcaccacct 3300ttcaattcca tggacctgat ttttccagaa agatgttttc ctctttcaga tttttgtaca 3360aggctaaaat gtctttccca tccataacca agtcctccta tgggtacata aacccaaagt 3420ccccacttct tttaaaggga tatgatcaag ttataacatg taccctgctt cccccaaccc 3480tgccttcttc actaaataag catgtagctc agtggtttcc aaatttggct gcacattcat 3540accaatcacc aggggatttt tttaaaatcc tgatgcccaa cttgcactcc acattaatta 3600acatgtctag gagtgggagc ctgacagaca ccactattaa aaaaaaaaaa aatccccaaa 3660atgattccaa tagacaacaa agttgaggaa ccactggcac atcccaagct aagatacaag 3720gttaaatggc ctttttaagt atgtcatact ggatctttaa ataaagcaag gcttttgtta 3780cactttgtca tgttattaaa agcagacctt tgggctgttt aaccgtgtaa caaaaatgcc 3840acgtgaaaaa taaaaatttt tattgtatag caattctcta taaatagtag ataatctaag 3900tccttatttt ctgatggctc ttgttccact attaacattg tttttaattt ttaaaatcct 3960atcagcagcc tcctaattag cagtgttagg aatttgcctt atgttttcca tctcatctcc 4020tgaacctgtt attctgagaa ctcataaata aaattcagcc aagattaatc aatcaatcaa 4080tcaatcagta gacgtcagag ataagcaact tttttttcca tttatttgaa ataatataca 4140agaatatagt gtgcaaaatt taggggcaac atcatgaaga agtgtgatga actgaaatca 4200attttacagc tgtgattcct aaccagaaac accacttggt aagtaacatg aaaagccatg 4260attgtagctc agagcaaaag cagctgtatt gccaatgtat ttgctctaat tttagacagt 4320tggaggaaaa ttaaagtgca agtgttgcac tgcagtaagt gcaaagtctg cccccaccat 4380aaagattatg atgacaaaat atatttaaga tacatggctg aggagataca gaacacgaag 4440ttaaaaaata caatggtgtt gactgtttgt taatagcacc attacagtga ctatatccca 4500atgctattaa ctaactttac cttggcctgg gctaggtctc cattggaaat aataacggat 4560ggctgctgcc acctggtgca tcaactcagc atgccatggt aactgcagca ggtggctctt 4620aggctgggac accaacacca gccacctgcc ccatgttctg gtagcctctt ggcactgacc 4680agactaggag cgcctatgtt tggcacagat gctgagccat gtggtggtta ctagaggaaa 4740ggccgactcc cagcttctgc ttcatttcat catgtgtaca atacagatta ataagcagta 4800aggagccaat gtataaacag cagttacata ttttttaaat tcccctttcg tacaatttaa 4860aataaaacat gtatacactt 4880127783DNAHomo sapiens 12aatacttgtt gcaataattg cccacgatag ctgctcaaac aagagagttg gaattcatct 60gtaaaaatca ctacatgtaa cgtaggagac aagaaaaata ttaatgacag aagatctgcg 120aacatgatgc acgtgaataa ttttcccttt agaaggcatt cctggatatg ttttgatgtg 180gacaatggca catctgcggg acggagtccc ttggatccca tgaccagccc aggatccggg 240ctaattctcc aagcaaattt tgtccacagt caacgacggg agtccttcct gtatcgatcc 300gacagcgatt atgacctctc tccaaagtct atgtcccgga actcctccat tgccagtgat 360atacacggag atgacttgat tgtgactcca tttgctcagg tcttggccag tctgcgaact 420gtacgaaaca actttgctgc attaactaat ttgcaagatc gagcacctag caaaagatca 480cccatgtgca accaaccatc catcaacaaa gccaccataa cagaggaggc ctaccagaaa 540ctggccagcg agaccctgga ggagctggac tggtgtctgg accagctaga gaccctacag 600accaggcact ccgtcagtga gatggcctcc aacaagttta aaaggatgct taatcgggag 660ctcacccatc tctctgaaat gagtcggtct ggaaatcaag tgtcagagtt tatatcaaac 720acattcttag ataagcaaca tgaagtggaa attccttctc caactcagaa ggaaaaggag 780aaaaagaaaa gaccaatgtc tcagatcagt ggagtcaaga aattgatgca cagctctagt 840ctgactaatt caagtatccc aaggtttgga gttaaaactg aacaagaaga tgtccttgcc 900aaggaactag aagatgtgaa caaatggggt cttcatgttt tcagaatagc agagttgtct 960ggtaaccggc ccttgactgt tatcatgcac accatttttc aggaacggga tttattaaaa 1020acatttaaaa ttccagtaga tactttaatt acatatctta tgactctcga agaccattac 1080catgctgatg tggcctatca caacaatatc catgctgcag atgttgtcca gtctactcat 1140gtgctattat ctacacctgc tttggaggct gtgtttacag atttggagat tcttgcagca 1200atttttgcca gtgcaataca tgatgtagat catcctggtg tgtccaatca atttctgatc 1260aatacaaact ctgaacttgc cttgatgtac aatgattcct cagtcttaga gaaccatcat 1320ttggctgtgg gctttaaatt gcttcaggaa gaaaactgtg acattttcca gaatttgacc 1380aaaaaacaaa gacaatcttt aaggaaaatg gtcattgaca tcgtacttgc aacagatatg 1440tcaaaacaca tgaatctact ggctgatttg aagactatgg ttgaaactaa gaaagtgaca 1500agctctggag ttcttcttct tgataattat tccgatagga ttcaggttct tcagaatatg 1560gtgcactgtg cagatctgag caacccaaca aagcctctcc agctgtaccg ccagtggacg 1620gaccggataa tggaggagtt cttccgccaa ggagaccgag agagggaacg tggcatggag 1680ataagcccca tgtgtgacaa gcacaatgct tccgtggaaa aatcacaggt gggcttcata 1740gactatattg ttcatcccct ctgggagaca tgggcagacc tcgtccaccc tgacgcccag 1800gatattttgg acactttgga ggacaatcgt gaatggtacc agagcacaat ccctcagagc 1860ccctctcctg cacctgatga cccagaggag ggccggcagg gtcaaactga gaaattccag 1920tttgaactaa ctttagagga agatggtgag tcagacacgg aaaaggacag tggcagtcaa 1980gtggaagaag acactagctg cagtgactcc aagactcttt gtactcaaga ctcagagtct 2040actgaaattc cccttgatga acaggttgaa gaggaggcag taggggaaga agaggaaagc 2100cagcctgaag cctgtgtcat agatgatcgt tctcctgaca cgtaacagtg caaaaacttt 2160catgcctttt ttttttttaa gtagaaaaat tgtttccaaa gtgcatgtca catgccacaa 2220ccacggtcac acctcactgt catctgccag gacgtttgtt gaacaaaact gaccttgact 2280actcagtcca gcgctcagga atatcgtaac cagttttttc acctccatgt catccgagca 2340aggtggacat cttcacgaac agcgttttta acaagatttc agcttggtag agctgacaaa 2400gcagataaaa tctactccaa attattttca agagagtgtg actcatcagg cagcccaaaa 2460gtttattgga cttggggttt ctattccttt ttatttgttt gcaatatttt cagaagaaag 2520gcattgcaca gagtgaactt aatggacgaa gcaacaaata tgtcaagaac aggacatagc 2580acgaatctgt taccagtagg aggaggatga gccacagaaa ttgcataatt ttctaatttc 2640aagtcttcct gatacatgac tgaatagtgt ggttcagtga gctgcactga cctctacatt 2700ttgtatgata tgtaaaacag attttttgta gagcttactt ttattattaa atgtattgag 2760gtattatatt taaaaaaaac tatgttcaga acttcatctg ccactggtta tttttttcta 2820aggagtaact tgcaagtttt cagtacaaat ctgtgctaca ctggataaaa atctaattta 2880tgaattttac ttgcacctta tagttcatag caattaactg atttgtagtg attcattgtt 2940tgttttatat accaatgact tccatatttt aaaagagaaa aacaacttta tgttgcagga 3000aacccttttt gtaagtcttt attatttact ttgcattttg tttcactctt tccagataag 3060cagagttgct cttcaccagt gtttttcttc atgtgcaaag tgactatttg ttctataata 3120cttttatgtg tgttatatca aatgtgtctt aagcttcatg caaactcagt catcagttcg 3180tgttgtctga agcaagtggg agatatataa atacccagta gctaaaatgg tcagtctttt 3240ttagatgttt tcctacttag tatctcctaa taacgttttg ctgtgtcact agatgttcat 3300ttcacaagtg catgtctttc taataatcca cacatttcat gctctaataa tccacacatt 3360tcatgctcat ttttattgtt tttacagcca gttatagtaa gaaaaaggtt tttccccttg 3420tgctgcttta taatttagcg tgtgtctgaa ccttatccat gtttgctaga tgaggtcttg 3480tcaaatatat cactaccatt gtcaccggtg aaaagaaaca ggtagttaag ttagggttaa 3540cattcatttc aaccacgagg ttgtatatca tgactagctt ttactcttgg tttacagaga 3600aaagttaaac agccaactag gcagttttta agaatattaa caatatatta acaaacacca 3660atacaactaa tcctatttgg ttttaatgat ttcaccatgg gattaagaac tatatcagga 3720acatccctga gaaacggttt taagtgtagc aactactctt ccttaatgga cagccacata 3780acgtgtagga agtcctttat cacttatcct cgatccataa gcatatcttg cagaggggaa 3840ctacttcttt aaacacatgg agggaaagaa gatgatgcca ctggcaccag agggttagta 3900ctgtgatgca tcctaaaata tttattatat tggtaaaaat tctggttaaa taaaaaatta 3960gagatcactc ttggctgatt tcagcaccag gaactgtatt acagttttag agattaattc 4020ctagtgttta cctgattata gcagttggca tcatggggca tttaattctg actttatccc 4080cacgtcagcc ttaataaagt cttctttacc ttctctatga agactttaaa gcccaaataa 4140tcatttttca cattgatatt caagaattga gatagataga agccaaagtg ggtatctgac 4200aagtggaaaa tcaaacgttt aagaagaatt acaactctga aaagcattta tatgtggaac 4260ttctcaagga gcctcctggg gactggaaag taagtcatca gccaggcaaa tgactcatgc 4320tgaagagagt ccccatttca gtcccctgag atctagctga tgcttagatc ctttgaaata 4380aaaattatgt ctttataact ctgatctttt acataaagca gaagaggaat caactagtta 4440attgcaaggt ttctactctg tttcctctgt aaagatcaga tggtaatctt tcaaataaga 4500aaaaaataaa gacgtatgtt tgaccaagta gtttcacaag aatatttggg aacttgtttc 4560ttttaatttt atttgtccct gagtgaagtc tagaaagaaa ggtaaagagt ctagagttta 4620ttcctctttc caaaacattc tcattcctct cctccctaca cttagtattt cccccacaga 4680gtgcctagaa tcttaataat gaataaaata aaaagcagca atatgtcatt aacaaatcca 4740gacctgaaag ggtaaagggt ttataactgc actaataaag agaggctctt tttttttctt 4800ccagtttgtt ggtttttaat ggtaccgtgt tgtaaagata cccactaatg gacaatcaaa 4860ttgcagaaaa ggctcaatat ccaagagaca gggactaatg cactgtacaa tctgcttatc 4920cttgcccttc tctcttgcca aagtgtgctt cagaaatata tactgcttta aaaaagaata 4980aaagaatatc cttttacaag tggctttaca tttcctaaaa tgccataaga aaatgcaata 5040tctgggtact gtatggggaa aaaaatgtcc aagtttgtgt aaaaccagtg catttcagct 5100tgcaagttac tgaacacaat aatgctgttt taattttgtt ttatatcagt taaaattcac 5160aataatgtag atagaacaaa ttacagacaa ggaaagaaaa aacttgaatg aaatggattt 5220tacagaaagc tttatgataa tttttgaatg cattatttat tttttgtgcc atgcattttt 5280tttctcacca aatgacctta cctgtaatac agtcttgttt gtctgtttac aaccatgtat 5340ttattgcaat gtacatactg taatgttaat tgtaaattat ctgttcttat taaaacatca 5400tcccatgatg ggatggtgtt gatatatttg gaaactcttg gtgagagaat gaatggtgtg 5460tatacatact ctgtacattt ttcttttctc ctgtaatata gtcttgtcac cttagagctt 5520gtttatggaa gattcaagaa aactataaaa tacttaaaga tatataaatt taaaaaaaca 5580tagctgcagg tctttggtcc cagggctgtg ccttaacttt aaccaatatt ttcttctgtt 5640ttgctgcatt tgaaaggtaa cagtggagct agggctgggc attttacatc caggctttta 5700attgattaga attctgccaa taggtggatt ttacaaaacc acagacaacc tctgaaagat 5760tctgagaccc ttttgagaca gaagctctta agtacttctt gccagggagc agcactgcat 5820gtgtgatggt tgtttgccat ctgttgatca ggaactactt cagctacttg catttgatta 5880tttccttttt tttttttttt aactcggaaa cacaactggg gaaatatatt ctttcccagt 5940gattataaac aatctttttc ttttttttaa gtccttttgg cttctagagc tcataggaaa 6000atggacttga tttgaaattg gagccagagt ttactcgtgt tggttatcta ttcatcagct 6060tcctgacatg ttaagagaat acattaaaga gaaaatactg ttttttaatc ctaaaatttt 6120tcttccacta agataaacca aatgtcctta catatatgta aacccatcta tttaaacgca 6180aaggtgggtt gatgtcagtt tacatagcag aaagcattca ctatcctcta agatttgttt 6240ctgcaaaact ttcattgctt tagaatttta aaatttcacc ttgtacaatg gccagcccct 6300aaagcaggaa acatttataa tggattatat ggaaacatcc tcccagtact tgcccagccc 6360ttgaatcatg tggcttttca gtgaaaggaa agattctttt tctaggaaaa atgagcctat 6420tttattttat tttattttat tttttgacac aaactgtaga ttttagcagc cctggcccaa 6480aggaatttga ttacttttgt tttaaacagt acaaagggga cactataatt acaaaaacat 6540ccttaactga tttgagttgt ttttatttct ttggatatat tttcagagtg gtaaattgtg 6600tgtgagaatt acaaatgatt attcttttag tggtttctta gcctctctta cagcccacgg 6660ggatagtact gtacatcaat accttcatat gaaattttta tatgcaatga aaataaaagc 6720atgggttgat tctgcctatt tatgactcaa tcttttacaa ataaaagatt attcatttta 6780aattatagtt caatcagcat gtctcttagg atactgaacg tggttgaaat gaaaggatag 6840tgacatcata agttagtact gatattcata accaaataaa gccaacttga gtaattttgc 6900tacattaaaa attaccaaaa ttacttagat ggcctataag attaagcatg gtgttttcta 6960agcaagcttt gaaaggggcc ttccatactt acttaattga atattctggg atattgaaaa 7020ttattcagat acttgacaat tatttttggt tacctactcc gcaaactaca aagttttaag 7080gactcaacaa taagttaatg agacacagtg tttgctttca tggagcttac agtctggagg 7140ggacaaaggc ttaaacaata ctcatataat tatatatgtg atcagtacaa tgaaggagct 7200cagtggggta aataagcagg aacctgaact tgatctgttc cggagggcca cagaaggctt 7260ccttgaggcc ttgagaaagt gatttgcatc tgagttctga aggattgtaa gaggtaacta 7320gggaaaaagt tgacaggaag aggaagggga tccagacaag aaacatttgc aaagatcttg 7380aggcataaat gagcttgaga catctggaga aactgaggaa aagtgagaga gtaggcaggg 7440cctggagccg cagagccatt gctaaccatc ctgtgtgaga tatcccccat tctgtagctt 7500tattctcata accctgctca attttcttta taacacttct cacagattta tatacgtgtt 7560tgtttttgtt atctgtctct cccaccagac cacagctcca tgagagcaag gtctttgctt 7620accaatatat cactagcact taaaactatg cctggtacac agtaggttct taatatgtgt 7680tgaatatagc catcaaattg atattggata taattcaatc tgataagata ttttgagata 7740ttaaagagtt tttaacttga taccataaaa aaaaaaaaaa aaa 778313551DNAHomo sapiens 13gagaggggta tacacaggga ggccaggcag cctggagtta gtcgaccgtt gcgagacgtt 60gagctgcggc agatgagtcc aaagccgaga gcctcgggac ctccggccaa ggccaaggag 120acaggaaaga ggaagtcctc ctctcagccg agccccagtg gcccgaagaa gaagactacc 180aaggtggccg agaagggaga agcagttcgt ggagggagac gcgggaagaa aggggctgcg 240acaaagatgg cggccgtgac ggcacctgag gcggagagcg ggccagcggc acccggcccc 300agcgaccagc ccagccagga gctccctcag cacgagctgc cgccggagga gccagtgagc 360gaggggaccc agcacgaccc cctgagtcag gagagcgagc tggaggaacc actgagtaag 420gggcgcccat ctactcccct atctccctga gcagcaacta agtttaggcc cagctgccag 480acctcagaga tctcaccagc agggtgcttc ccatgttgat gacaataaaa tgaatgtgtt 540gcaaaccgaa a 551

Claims

1. A method of assessing whether an individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising establishing, by determining the expression level of two more genes selected from the group consisting of: K(lysine) acetyltransferase 2B gene (KAT2B); calcium/calmodulin-dependent serine protein kinase 3 gene (CASK); ATP-binding cassette sub-family D member 2 gene (ABCD2); disks large homolog 1 gene (DLG1); synovial sarcoma translocation, chromosome 18 gene (SS18); Retinoblastoma-like protein 2 gene (RBL2); RAS oncogene family-like 1 gene (RAB7L1); methylenetetrahydrofolate dehydrogenase 1 gene (MTHFD1); keratocan gene (KERA); B cell-specific Moloney murine leukemia virus integration site 1 gene (BMI1); conserved oligomeric Golgi complex subunit 5 gene (COG5); cAMP-specific 3',5'-cyclic phosphodiesterase 4D gene (PDE4D); and variable charge, Y-linked gene (VCY); in a sample obtained from the individual, whether said subject has said phenotype, wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype.

2. A method of assessing whether an individual is at high risk or low risk of autoimmune disease progression, the method comprising either: (A) determining whether the individual has an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype using the method of claim 1, wherein the presence of said phenotype indicates that the individual is at low risk of autoimmune disease progression, and wherein the absence of said phenotype indicates that the individual is at high risk of autoimmune disease progression; OR: (B) determining whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising: (i) providing a PBMC sample obtained from the individual; (ii) extracting mRNA from the PBMC sample; (iii) performing reverse transcription quantitative PCR (RT-qPCR) to convert the mRNA into cDNA and determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY, wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype, and wherein the presence of said phenotype indicates that the individual is at low risk of autoimmune disease progression, and wherein the absence of said phenotype indicates that the individual is at high risk of autoimmune disease progression.

3. The method according to claim 2, wherein the autoimmune disease is not rheumatoid arthritis (RA) or inflammatory bowel disease (IBD).

4. The method according to claim 3, wherein the autoimmune disease is selected from the group consisting of: ANCA-associated vasculitis (AAV), systemic lupus erythematosus (SLE), type 1 diabetes, and idiopathic pulmonary fibrosis (IPF).

5. The method according to claim 4, wherein the autoimmune disease is AAV or SLE, and wherein an individual who is at low risk of autoimmune disease progression is at low risk of relapses or flares of the disease, and wherein an individual who is at high risk of autoimmune disease progression is at high risk of relapses or flares of the disease.

6. The method according to claim 4, wherein the autoimmune disease is type 1 diabetes, and wherein an individual who is at low risk of autoimmune disease progression is at low risk of progressing to type 1 diabetes, and wherein an individual who is at high risk of autoimmune disease progression is at high risk of progressing to type 1 diabetes.

7. The method according to claim 4, wherein the autoimmune disease is IPF, and wherein an individual who is at low risk of autoimmune disease progression is at low risk of ongoing reduction of lung function, and wherein an individual who is at high risk of autoimmune disease progression is at high risk of ongoing reduction of lung function.

8. The method according to claim 2, further comprising: (ii) selecting an individual identified as one who is at high risk or low risk of autoimmune disease progression for treatment for the autoimmune disease.

9. The method according to claim 2, further comprising: (ii) subjecting an individual identified as one who is at high risk or low risk of autoimmune disease progression to treatment for the autoimmune disease.

10. The method according to claim 8, wherein the treatment comprises inducing an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype in the individual.

11. The method according to claim 8, wherein an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype is induced in the individual by administering a therapeutically effective amount of a programmed cell death protein 1 (PD-1) ligand.

12. The method according to claim 11, wherein the PD-1 ligand is programmed death-ligand 1 (PDL-1).

13. The method according to claim 8, wherein the autoimmune disease is AAV or SLE and wherein individual has been identified as one who is at high risk of autoimmune disease progression, wherein the treatment comprises treatment with a more frequent or more intense disease treatment regimen, or with a disease regimen not normally administered during the maintenance phase of the autoimmune disease.

14. The method according to claim 8, wherein the autoimmune disease is AAV or SLE and wherein individual has been identified as one who is at low risk of autoimmune disease progression, wherein the treatment comprises treatment with a less frequent or less intense disease treatment regimen, or with a disease regimen not normally administered during the maintenance phase of the autoimmune disease.

15. The method according to claim 8, wherein individual has been identified as one who is at high risk of progressing to type 1 diabetes, wherein the treatment comprises a prophylactic treatment for type 1 diabetes.

16. The method according to claim 8, wherein the autoimmune disease is IPF and wherein individual has been identified as one who is at high risk of autoimmune disease progression, wherein the treatment comprises treatment with nintedanib, pirfenidone, a phosphodiesterase inhibitor, or immunosuppressive therapy.

17. An in vitro method of assessing whether CD8.sup.+ and CD4.sup.+ T cells in a sample have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, the method comprising establishing, by determining the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY, whether said phenotype is present, wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY relative to the level of expression of these genes in a sample of CD8.sup.+ and CD4.sup.+ T cells which do not have said phenotype.

18. The in vitro method according to claim 17, wherein said expression level of the two or more genes is determined using reverse-transcription quantitative PCR (RT-qPCR), microarray analysis, enzyme-linked immunosorbent assays (ELISA), protein chips, flow cytometry (such as Flow-FISH for RNA, also referred to as FlowRNA), mass spectrometry, Western blotting, or northern blotting.

19. A method of assessing medical risk in an individual, wherein the assessment is of (A) whether an individual with a chronic infection is at high risk or low risk of progression of said chronic infection; OR (B) whether an individual is at high risk or low risk of not mounting an effective immune response to a vaccine against a disease, the individual having received the vaccination; OR (C) whether an individual is at high risk or low risk of infection-associated immunopathology; OR (D) whether an individual is at high risk or low risk of transplant rejection; OR (E) assessing whether an individual is at high risk or low risk of cancer progression; the method comprising either: (i) determining whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, said method being performed by using the method of claim 1; OR determining whether the individual has or does not have an exhausted CD8.sup.+ T cell or lack of CD4.sup.+ T cell costimulation phenotype, by: (ii) providing a PBMC sample obtained from the individual; (iii) extracting mRNA from the PBMC sample; (iv) performing reverse transcription quantitative PCR (RT-qPCR) to convert the mRNA into cDNA and determine the expression level of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY, wherein said phenotype is characterised by downregulated expression of genes KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, BMI1, COG5, and PDE4D, and upregulated expression of genes KERA and VCY, relative to the level of expression of these genes in an individual who does not have said phenotype, and wherein the presence of said phenotype indicates in (A) that the individual is at high risk of progression of said chronic infection, and wherein the absence of said phenotype indicates in (A) that the individual is at low risk of progression of said chronic infection; wherein the presence of said phenotype indicates in (B) that the individual at high risk of not mounting effective immune response to the vaccination, and wherein the absence of said phenotype indicates in (B) that the individual is at low risk of not mounting effective immune response to the vaccination; wherein the presence of said phenotype indicates in (C) that the individual is at low risk of infection-associated immunopathology, and wherein the absence of said phenotype indicates in (C) that the individual is at high risk of infection-associated immunopathology; wherein the presence of said phenotype indicates in (D) that the individual is at low risk of transplant rejection, and wherein the absence of said phenotype indicates in (D) that the individual is at high risk of transplant rejection; wherein the presence of said phenotype indicates in (E) that the individual is at high risk of cancer progression, and wherein the absence of said phenotype indicates in (E) that the individual is at low risk of cancer progression.

20. The method as defined in claim 19, performed on a system comprising a tool or tools for determining expression of two more genes selected from the group consisting of: KAT2B, CASK, ABCD2, DLG1, SS18, RBL2, RAB7L1, MTHFD1, KERA, BMI1, COG5, PDE4D, and VCY; and a computer programmed to compute a risk score of the risk of the individual not responding to the treatment from the gene expression data of the subject.